diff --git a/orthohmm/args_processing.py b/orthohmm/args_processing.py index 133cf7f..4a2d658 100644 --- a/orthohmm/args_processing.py +++ b/orthohmm/args_processing.py @@ -8,6 +8,7 @@ from .helpers import ( StartStep, StopStep, + SubstitutionMatrix, ) @@ -71,6 +72,8 @@ def process_args(args) -> dict: start = StartStep(args.start) if args.start else None stop = StopStep(args.stop) if args.stop else None + substitution_matrix = SubstitutionMatrix(args.substitution_matrix) if args.substitution_matrix else SubstitutionMatrix.blosum62 + return dict( fasta_directory=fasta_directory, output_directory=output_directory, @@ -81,4 +84,5 @@ def process_args(args) -> dict: inflation_value=float(inflation_value), start=start, stop=stop, + substitution_matrix=substitution_matrix, ) diff --git a/orthohmm/externals.py b/orthohmm/externals.py index fdc35ad..6f60fe6 100644 --- a/orthohmm/externals.py +++ b/orthohmm/externals.py @@ -1,4 +1,3 @@ -import itertools import multiprocessing import subprocess from typing import List diff --git a/orthohmm/helpers.py b/orthohmm/helpers.py index df08f81..b7c55d9 100644 --- a/orthohmm/helpers.py +++ b/orthohmm/helpers.py @@ -23,6 +23,18 @@ class StartStep(Enum): search_res = "search_res" +class SubstitutionMatrix(Enum): + blosum45 = "BLOSUM45" + blosum50 = "BLOSUM50" + blosum62 = "BLOSUM62" + blosum80 = "BLOSUM80" + blosum90 = "BLOSUM90" + pam30 = "PAM30" + pam70 = "PAM70" + pam120 = "PAM120" + pam240 = "PAM240" + + def generate_phmmer_cmds( files: List[str], phmmer: str, @@ -30,14 +42,15 @@ def generate_phmmer_cmds( fasta_directory: str, cpu: int, stop: str, + substitution_matrix: SubstitutionMatrix, ): pairwise_combos = list(itertools.product(files, repeat=2)) phmmer_cmds = [] for combo in pairwise_combos: if stop == "prepare": - phmmer_cmds.append(f"{phmmer} --noali --notextw --cpu {cpu} --tblout {output_directory}/orthohmm_working_res/{combo[0]}_2_{combo[1]}.phmmerout.txt {fasta_directory}/{combo[0]} {fasta_directory}/{combo[1]}") + phmmer_cmds.append(f"{phmmer} --mx {substitution_matrix.value} --noali --notextw --cpu {cpu} --tblout {output_directory}/orthohmm_working_res/{combo[0]}_2_{combo[1]}.phmmerout.txt {fasta_directory}/{combo[0]} {fasta_directory}/{combo[1]}") else: - phmmer_cmds.append(f"{phmmer} --noali --notextw --tblout {output_directory}/orthohmm_working_res/{combo[0]}_2_{combo[1]}.phmmerout.txt {fasta_directory}/{combo[0]} {fasta_directory}/{combo[1]}") + phmmer_cmds.append(f"{phmmer} --mx {substitution_matrix.value} --noali --notextw --tblout {output_directory}/orthohmm_working_res/{combo[0]}_2_{combo[1]}.phmmerout.txt {fasta_directory}/{combo[0]} {fasta_directory}/{combo[1]}") return phmmer_cmds diff --git a/orthohmm/orthohmm.py b/orthohmm/orthohmm.py index 3ebcb9b..c764593 100644 --- a/orthohmm/orthohmm.py +++ b/orthohmm/orthohmm.py @@ -19,6 +19,7 @@ generate_phmmer_cmds, StartStep, StopStep, + SubstitutionMatrix, ) from .parser import create_parser from .writer import ( @@ -39,6 +40,7 @@ def execute( inflation_value: float, start: Union[StartStep, None], stop: Union[StopStep, None], + substitution_matrix: SubstitutionMatrix, **kwargs, ) -> None: # for reporting runtime duration to user @@ -60,6 +62,7 @@ def execute( fasta_directory, cpu, stop, + substitution_matrix, ) # print phmmer cmds and exit is users only want to prepare phmmer cmds @@ -79,6 +82,7 @@ def execute( files, start, stop, + substitution_matrix, ) # set current step and determine the total number of diff --git a/orthohmm/parser.py b/orthohmm/parser.py index d8345cd..3e1656d 100644 --- a/orthohmm/parser.py +++ b/orthohmm/parser.py @@ -9,7 +9,7 @@ from .helpers import ( StartStep, - StopStep + StopStep, ) from .version import __version__ @@ -71,6 +71,10 @@ def create_parser() -> ArgumentParser: -p, --phmmer path to phmmer from HMMER suite (default: phmmer) + -x, --substitution_matrix substitution matrix to use for + residue probabilities + (default: BLOSUM62) + -c, --cpu number of parallel CPU workers to use for multithreading (default: auto detect) @@ -106,6 +110,12 @@ def create_parser() -> ArgumentParser: is assumed to be in the PATH variable; in other words, phmmer can be evoked by typing `phmmer`. + Substitution matrix (-x, --substitution_matrix) + Residue alignment probabilities will be determined from the + specified substitution matrix. Supported substitution matrices + include: BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM90, + PAM30, PAM70, PAM120, and PAM240. + CPU (-c, --cpu) Number of CPU workers for multithreading during sequence search. This argument is used by phmmer during all-by-all comparisons. @@ -171,7 +181,9 @@ def create_parser() -> ArgumentParser: orthohmm_working_res Various intermediate results files that help OrthoHMM start analyses - from an intermediate step in the analysis + from an intermediate step in the analysis. This includes outputs + from phmmer searches, initial edges inputted to MCL, and the + output from MCL clustering. """ # noqa ), ) @@ -183,6 +195,17 @@ def create_parser() -> ArgumentParser: metavar="output_directory" ) + substitution_matrix_choices = [step.value for step in StartStep] + optional.add_argument( + "-x", + "--substitution_matrix", + type=str, + required=False, + help=SUPPRESS, + metavar="substitution_model", + choices=substitution_matrix_choices, + ) + optional.add_argument( "-s", "--single_copy_threshold", diff --git a/orthohmm/writer.py b/orthohmm/writer.py index b0a3acc..c095e08 100644 --- a/orthohmm/writer.py +++ b/orthohmm/writer.py @@ -2,7 +2,11 @@ import time from typing import List, Union -from .helpers import StartStep, StopStep +from .helpers import ( + StartStep, + StopStep, + SubstitutionMatrix, +) from .version import __version__ @@ -16,6 +20,7 @@ def write_user_args( files: List[str], start: Union[StartStep, None], stop: Union[StopStep, None], + substitution_matrix: SubstitutionMatrix, ) -> None: try: @@ -51,6 +56,7 @@ def write_user_args( Step to start analysis: {start_print} Step to stop analysis: {stop_print} Path to phmmer: {phmmer} + Substitution matrix: {substitution_matrix.value} Path to mcl: {mcl} Single-copy threshold: {single_copy_threshold} CPUs: {cpu} diff --git a/tests/integration/test_simple_case.py b/tests/integration/test_simple_case.py index 70c7495..1a79964 100644 --- a/tests/integration/test_simple_case.py +++ b/tests/integration/test_simple_case.py @@ -4,6 +4,7 @@ from orthohmm.orthohmm import execute +from orthohmm.helpers import SubstitutionMatrix here = Path(__file__) @@ -25,6 +26,7 @@ def test_simple_case(self): inflation_value=1.5, start=None, stop=None, + substitution_matrix=SubstitutionMatrix.blosum62, ) execute(**kwargs) diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index b0f136e..e9596a6 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ WBGene00013724.1 - WBGene00013724.1 - 9.1e-152 489.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 683347c..7cb2375 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ ENSCAFP00000048558 - WBGene00013724.1 - 4.3e-60 190.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 53e006e..87418ae 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ ENSCINP00000010262 - WBGene00013724.1 - 4.1e-65 207.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index c370601..edc0c92 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -12,7 +12,7 @@ ENSDARP00000149121 - WBGene00013724.1 - 4e-50 159.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 4920c92..110d34a 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ ENSGALP00000028084 - WBGene00013724.1 - 1.8e-65 208.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index da1aa45..aad4c37 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ ENSP00000340836 - WBGene00013724.1 - 4.7e-68 216.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 59a6424..0aba790 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ ENSMODP00000002384 - WBGene00013724.1 - 1.8e-68 218.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index a0f6920..8a5c53c 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ ENSMUSP00000025631 - WBGene00013724.1 - 3.7e-67 214.7 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 438e48a..d394401 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ ENSPTRP00000079818 - WBGene00013724.1 - 4.7e-68 216.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index ca525d2..cbb283b 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSRNOP00000016871 - WBGene00013724.1 - 4e-68 217.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 1d66bd0..73d799c 100644 --- a/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ ENSTNIP00000019800 - WBGene00013724.1 - 2.2e-65 208.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 797d521..98314ad 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ WBGene00013724.1 - ENSCAFP00000048558 - 1.3e-60 192.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 2308e5a..29dfcd8 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCAFP00000017344 - ENSCAFP00000017344 - 0 5307.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 1acba0f..11e65d7 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCINP00000024362 - ENSCAFP00000017344 - 1.3e-291 958.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 4631723..1f24827 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSDARP00000129655 - ENSCAFP00000017344 - 0 3406.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 44186fe..47fb3be 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSGALP00000046461 - ENSCAFP00000017344 - 0 4126.1 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 9690723..bfbf686 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSP00000260197 - ENSCAFP00000017344 - 0 4968.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 89d42ac..c790a7c 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMODP00000016287 - ENSCAFP00000017344 - 0 4656.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 2b0d084..77a9275 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMUSP00000058613 - ENSCAFP00000017344 - 0 4829.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 91e9927..ad399bc 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSPTRP00000007532 - ENSCAFP00000017344 - 0 4983.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 254c08d..3c7c66f 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSRNOP00000016871 - ENSCAFP00000048558 - 1.4e-125 407.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index f84647e..b87affb 100644 --- a/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSTNIP00000017394 - ENSCAFP00000017344 - 0 3325.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 14b4c72..eea0d32 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ WBGene00013724.1 - ENSCINP00000010262 - 2.5e-65 207.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 8e8d9d5..67deade 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCAFP00000017344 - ENSCINP00000024362 - 1.5e-292 961.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 7bc1d01..a4b96a2 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCINP00000024362 - ENSCINP00000024362 - 0 3552.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 131bca0..3ad6b0b 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSDARP00000129655 - ENSCINP00000024362 - 1.3e-283 932.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index c3a3844..6ccfbf8 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSGALP00000046461 - ENSCINP00000024362 - 1.3e-293 964.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index c371578..7403b51 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSP00000260197 - ENSCINP00000024362 - 2.3e-288 947.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index bc7758b..4602977 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMODP00000016287 - ENSCINP00000024362 - 3.7e-297 976.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 80730af..aadada1 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMUSP00000058613 - ENSCINP00000024362 - 5.2e-290 953.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 6c1eb8d..5e01e71 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSPTRP00000007532 - ENSCINP00000024362 - 4.7e-288 946.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 355b1c2..60edba1 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSRNOP00000016871 - ENSCINP00000010262 - 4.5e-74 236.7 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 5d230b0..c86d28a 100644 --- a/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSTNIP00000017394 - ENSCINP00000024362 - 1.3e-279 918.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 87d108e..f49f3cc 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -12,7 +12,7 @@ WBGene00013724.1 - ENSDARP00000149121 - 2.2e-51 161.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 13b92c9..5e853e2 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSCAFP00000017344 - ENSDARP00000129655 - 0 3409.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index bed72d5..a2ed816 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSCINP00000024362 - ENSDARP00000129655 - 2e-284 934.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 1605cfb..70f43c3 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -21,7 +21,7 @@ ENSDARP00000129655 - ENSDARP00000129655 - 0 5322.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index a2fcbb4..b3d6800 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSGALP00000046461 - ENSDARP00000129655 - 0 3423.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 19a8e47..9cbc185 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSP00000260197 - ENSDARP00000129655 - 0 3439.1 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index d56eb8a..56c4367 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSMODP00000016287 - ENSDARP00000129655 - 0 3474.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index c6bf206..08deb0f 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSMUSP00000058613 - ENSDARP00000129655 - 0 3430.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index c9ef9fb..c1b7d01 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSPTRP00000007532 - ENSDARP00000129655 - 0 3439.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 3332e0d..6f21135 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -15,7 +15,7 @@ ENSRNOP00000016871 - ENSDARP00000149121 - 6.6e-104 333.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index b0f8e84..b8c2761 100644 --- a/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSTNIP00000017394 - ENSDARP00000129655 - 0 4009.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 384256b..30ac8fb 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ WBGene00013724.1 - ENSGALP00000028084 - 3.7e-66 210.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 03e5516..fa915df 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCAFP00000017344 - ENSGALP00000046461 - 0 4127.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index c327586..e01a8ff 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCINP00000024362 - ENSGALP00000046461 - 1.2e-290 954.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index ddac7cc..2025bf1 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSDARP00000129655 - ENSGALP00000046461 - 0 3421.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 276a6b0..130c517 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSGALP00000046461 - ENSGALP00000046461 - 0 5310.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index beec299..b13cfc4 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSP00000260197 - ENSGALP00000046461 - 0 4163.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 7d557d2..35905f8 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMODP00000016287 - ENSGALP00000046461 - 0 4256.1 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 0b663c3..51a4da0 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMUSP00000058613 - ENSGALP00000046461 - 0 4101.1 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 1337ad0..77f3ce3 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSPTRP00000007532 - ENSGALP00000046461 - 0 4174.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 3177dca..1c3a9a9 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSRNOP00000016871 - ENSGALP00000028084 - 4.1e-141 457.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 2744d44..2736e5d 100644 --- a/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSTNIP00000017394 - ENSGALP00000046461 - 0 3326.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 8f30421..86823b6 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ WBGene00013724.1 - ENSP00000340836 - 1e-68 218.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index ef26154..cee4069 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCAFP00000017344 - ENSP00000260197 - 0 4969.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index cdbfddb..b7339d5 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCINP00000024362 - ENSP00000260197 - 2.3e-288 947.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index f7d8559..20920dd 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSDARP00000129655 - ENSP00000260197 - 0 3436.1 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index d99c184..1443b5d 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSGALP00000046461 - ENSP00000260197 - 0 4163.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 7716e4f..4045386 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSP00000260197 - ENSP00000260197 - 0 5330.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index d8d5a79..54a544e 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMODP00000016287 - ENSP00000260197 - 0 4737.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index b9e9779..6af8234 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMUSP00000058613 - ENSP00000260197 - 0 4997.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 86ad2fd..f16154e 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSPTRP00000007532 - ENSP00000260197 - 0 5306.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 9dee746..d77885a 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSRNOP00000016871 - ENSP00000340836 - 1.1e-145 470.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index ff93e30..7b50633 100644 --- a/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSTNIP00000017394 - ENSP00000260197 - 0 3327.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:46 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index a800bb2..65a3d53 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ WBGene00013724.1 - ENSMODP00000002384 - 5.2e-69 219.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:58 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index fef23de..59fb12b 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCAFP00000017344 - ENSMODP00000016287 - 0 4656.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 4002a61..ffd6970 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCINP00000024362 - ENSMODP00000016287 - 1.3e-288 947.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:58 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 661ec98..4dd4787 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSDARP00000129655 - ENSMODP00000016287 - 0 3471.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 7722d58..b04d5f3 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSGALP00000046461 - ENSMODP00000016287 - 0 4255.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:58 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index ce51a7a..5f370ec 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSP00000260197 - ENSMODP00000016287 - 0 4737.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:58 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 1f65f26..1e524d8 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMODP00000016287 - ENSMODP00000016287 - 0 5338.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:58 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 74e5994..f7302ca 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMUSP00000058613 - ENSMODP00000016287 - 0 4649.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 971c338..97b9b3a 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSPTRP00000007532 - ENSMODP00000016287 - 0 4745.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index f8f541d..0eb546d 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSRNOP00000016871 - ENSMODP00000002384 - 3.7e-145 468.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:58 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 0b43e69..eaa7f34 100644 --- a/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSTNIP00000017394 - ENSMODP00000016287 - 0 3367.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:57 2024 +# Date: Fri Aug 23 14:08:48 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index bc16ef0..69fdbd8 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ WBGene00013724.1 - ENSMUSP00000025631 - 4.9e-68 215.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:53 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index f87ff00..36641ad 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCAFP00000017344 - ENSMUSP00000058613 - 0 4829.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:53 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 4e5b133..39e4819 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCINP00000024362 - ENSMUSP00000058613 - 9.1e-293 961.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 132a3af..93439e3 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSDARP00000129655 - ENSMUSP00000058613 - 0 3427.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:53 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 29139b4..13a3ea0 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSGALP00000046461 - ENSMUSP00000058613 - 0 4100.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 84b8851..70bf269 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSP00000260197 - ENSMUSP00000058613 - 0 4997.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:53 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 424246a..f5d3f8a 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMODP00000016287 - ENSMUSP00000058613 - 0 4649.4 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index ccc2067..61b256a 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -14,7 +14,7 @@ ENSMUSP00000058613 - ENSMUSP00000058613 - 0 5320.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:53 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 3d7f854..27123d4 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSPTRP00000007532 - ENSMUSP00000058613 - 0 5013.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:53 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index fdf5c5f..6f8d151 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -12,7 +12,7 @@ ENSRNOP00000065522 - ENSMUSP00000086314 - 7.7e-256 838.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:53 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index b2fce20..9afab2f 100644 --- a/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSTNIP00000017394 - ENSMUSP00000058613 - 0 3345.1 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:53 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 3a1d4c7..745ed1a 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ WBGene00013724.1 - ENSPTRP00000079818 - 1e-68 218.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index c42cb5a..3bf1ef9 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCAFP00000017344 - ENSPTRP00000007532 - 0 4983.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 2a2ef0a..6a62a76 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCINP00000024362 - ENSPTRP00000007532 - 2.7e-288 947.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 8d83a9b..303eaf1 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSDARP00000129655 - ENSPTRP00000007532 - 0 3436.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 1fdbfa3..fc31ea5 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSGALP00000046461 - ENSPTRP00000007532 - 0 4173.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index d8eb2d0..3086aed 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSP00000260197 - ENSPTRP00000007532 - 0 5306.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index e1ca085..e2d61c6 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMODP00000016287 - ENSPTRP00000007532 - 0 4745.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 40150cf..6b7ed43 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMUSP00000058613 - ENSPTRP00000007532 - 0 5013.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index db1efa2..522cd87 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSPTRP00000007532 - ENSPTRP00000007532 - 0 5329.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 739c413..fdc929f 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSRNOP00000016871 - ENSPTRP00000079818 - 1.1e-145 470.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index c83f8cf..621fa6c 100644 --- a/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSTNIP00000017394 - ENSPTRP00000007532 - 0 3331.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Pan_troglodytes.Pan_tro_3.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 7d10fb8..ab8feee 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ WBGene00013724.1 - ENSRNOP00000016871 - 6.5e-69 218.7 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index e5f5815..1ff96e8 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCAFP00000048558 - ENSRNOP00000016871 - 2.7e-126 406.8 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 7234636..85c6815 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCINP00000010262 - ENSRNOP00000016871 - 1.6e-74 237.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index 3603c1f..bec3a5d 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -15,7 +15,7 @@ ENSDARP00000149121 - ENSRNOP00000016871 - 1.9e-103 333.1 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 6a0f4db..cb8b2ff 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSGALP00000028084 - ENSRNOP00000016871 - 9.8e-142 457.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index 1f25ad5..c3d054f 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSP00000340836 - ENSRNOP00000016871 - 8e-146 470.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index 0050095..4791977 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMODP00000002384 - ENSRNOP00000016871 - 2.3e-145 469.1 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 82cff95..d2f5a64 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -12,7 +12,7 @@ ENSMUSP00000086311 - ENSRNOP00000065522 - 1.9e-255 836.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 363d658..f4416d4 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSPTRP00000079818 - ENSRNOP00000016871 - 8e-146 470.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 0396701..d19f700 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSRNOP00000065522 - ENSRNOP00000065522 - 0 1213.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index 651547e..cbd5cdd 100644 --- a/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSTNIP00000019800 - ENSRNOP00000016871 - 3.1e-130 419.6 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Rattus_norvegicus.Rnor_6.0.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:56 2024 +# Date: Fri Aug 23 14:08:47 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt index 4bbf035..2757c93 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt @@ -9,7 +9,7 @@ WBGene00013724.1 - ENSTNIP00000019800 - 6.1e-66 209.0 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt index 370c268..a1687c1 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCAFP00000017344 - ENSTNIP00000017394 - 0 3329.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt index 6c83a83..e4810a8 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSCINP00000024362 - ENSTNIP00000017394 - 4.9e-284 933.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt index c40f6bb..2279138 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt @@ -13,7 +13,7 @@ ENSDARP00000129655 - ENSTNIP00000017394 - 0 4011.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt index 9b6dee4..0333a1f 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSGALP00000046461 - ENSTNIP00000017394 - 0 3328.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt index f3f9f7a..41192ed 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSP00000260197 - ENSTNIP00000017394 - 0 3332.1 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt index c67e0d3..8f3f78f 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMODP00000016287 - ENSTNIP00000017394 - 0 3370.7 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:55 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt index 6482baa..0fee573 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSMUSP00000058613 - ENSTNIP00000017394 - 0 3349.3 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:44 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt index 564349c..05c428a 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSPTRP00000007532 - ENSTNIP00000017394 - 0 3336.2 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt index 4f6ae07..320f3e7 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSRNOP00000016871 - ENSTNIP00000019800 - 5e-130 419.5 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt index e81bfba..906009b 100644 --- a/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt +++ b/tests/samples/orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt @@ -10,7 +10,7 @@ ENSTNIP00000017394 - ENSTNIP00000017394 - 0 5341.9 # Pipeline mode: SEARCH # Query file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Target file: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa -# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli/tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Wed Aug 21 11:32:54 2024 +# Date: Fri Aug 23 14:08:45 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/orthohmm_edges.txt b/tests/samples/orthohmm_working_res/orthohmm_edges.txt index b68c0fd..0e77408 100644 --- a/tests/samples/orthohmm_working_res/orthohmm_edges.txt +++ b/tests/samples/orthohmm_working_res/orthohmm_edges.txt @@ -1,181 +1,181 @@ ENSMUSP00000086311 ENSMUSP00000086314 0.9452235456218643 ENSMUSP00000032440 ENSCAFP00000053904 1.1765339326216484 -ENSCAFP00000017344 ENSMUSP00000058613 1.1191809742240841 -ENSMUSP00000032440 ENSTNIP00000005325 1.1230455740952423 -ENSTNIP00000019800 ENSMUSP00000025631 1.0573543116888735 -ENSTNIP00000017394 ENSMUSP00000058613 0.8204945552781063 -ENSMUSP00000032440 ENSPTRP00000071151 0.9750143971399228 +ENSMUSP00000058613 ENSCAFP00000017344 1.1191809742240841 +ENSTNIP00000005325 ENSMUSP00000032440 1.1230455740952423 +ENSMUSP00000025631 ENSTNIP00000019800 1.0573543116888735 +ENSMUSP00000058613 ENSTNIP00000017394 0.8204945552781063 +ENSPTRP00000071151 ENSMUSP00000032440 0.9750143971399228 ENSPTRP00000079818 ENSMUSP00000025631 0.9947457998525575 -ENSPTRP00000007532 ENSMUSP00000058613 1.0305438528225042 +ENSMUSP00000058613 ENSPTRP00000007532 1.0305438528225042 ENSDARP00000071531 ENSMUSP00000032440 1.1405390347688653 -ENSMUSP00000032440 ENSDARP00000147265 1.109983290000416 -ENSMUSP00000032440 ENSDARP00000154605 1.1083231295307774 -ENSDARP00000110254 ENSMUSP00000025631 1.014393194490703 -ENSDARP00000149121 ENSMUSP00000025631 0.8935016279742156 +ENSDARP00000147265 ENSMUSP00000032440 1.109983290000416 +ENSDARP00000154605 ENSMUSP00000032440 1.1083231295307774 +ENSMUSP00000025631 ENSDARP00000110254 1.014393194490703 +ENSMUSP00000025631 ENSDARP00000149121 0.8935016279742156 ENSDARP00000129655 ENSMUSP00000058613 0.8464014718555611 -ENSP00000373312 ENSMUSP00000032440 0.9739080572466866 +ENSMUSP00000032440 ENSP00000373312 0.9739080572466866 ENSP00000340836 ENSMUSP00000025631 0.996854926953224 ENSP00000260197 ENSMUSP00000058613 1.029618128104977 ENSMUSP00000032440 WBGene00003806.1 0.9330346205728083 -WBGene00013724.1 ENSMUSP00000025631 1.078616751331466 +ENSMUSP00000025631 WBGene00013724.1 1.078616751331466 ENSMUSP00000032440 ENSRNOP00000014377 1.1575744132634167 ENSRNOP00000016871 ENSMUSP00000025631 1.118452164541046 ENSRNOP00000065522 ENSMUSP00000086314 0.724492027798829 -ENSCINP00000005198 ENSMUSP00000032440 1.524489076894231 +ENSMUSP00000032440 ENSCINP00000005198 1.524489076894231 ENSCINP00000010262 ENSMUSP00000025631 0.998945905307546 ENSCINP00000024362 ENSMUSP00000058613 0.4807572315142691 -ENSGALP00000028084 ENSMUSP00000025631 0.981655351115904 -ENSGALP00000046461 ENSMUSP00000058613 1.0971675453571852 +ENSMUSP00000025631 ENSGALP00000028084 0.981655351115904 +ENSMUSP00000058613 ENSGALP00000046461 1.0971675453571852 ENSMUSP00000032440 ENSMODP00000006811 1.035122951917207 ENSMODP00000002384 ENSMUSP00000025631 1.001174747698835 -ENSMODP00000016287 ENSMUSP00000058613 0.9642127408498951 +ENSMUSP00000058613 ENSMODP00000016287 0.9642127408498951 ENSCAFP00000048558 ENSMUSP00000025631 0.7048020506658835 ENSTNIP00000005325 ENSCAFP00000053904 1.29041322599113 ENSCAFP00000048558 ENSTNIP00000019800 0.773726752517809 -ENSCAFP00000017344 ENSTNIP00000017394 0.9375675734980686 +ENSTNIP00000017394 ENSCAFP00000017344 0.9375675734980686 ENSPTRP00000071151 ENSCAFP00000053904 1.1117442428910387 -ENSCAFP00000048558 ENSPTRP00000079818 0.7222433706443235 +ENSPTRP00000079818 ENSCAFP00000048558 0.7222433706443235 ENSCAFP00000017344 ENSPTRP00000007532 1.1666255159560786 ENSDARP00000147265 ENSCAFP00000053904 1.2662879716451452 ENSDARP00000154605 ENSCAFP00000053904 1.264976532704249 ENSDARP00000071531 ENSCAFP00000053904 1.2961637997082234 ENSCAFP00000048558 ENSDARP00000110254 0.7495847510861663 -ENSCAFP00000017344 ENSDARP00000129655 0.9559051251977784 -ENSP00000373312 ENSCAFP00000053904 1.110881900680476 -ENSCAFP00000048558 ENSP00000340836 0.7239183668098337 -ENSCAFP00000017344 ENSP00000260197 1.1659756100193193 +ENSDARP00000129655 ENSCAFP00000017344 0.9559051251977784 +ENSCAFP00000053904 ENSP00000373312 1.110881900680476 +ENSP00000340836 ENSCAFP00000048558 0.7239183668098337 +ENSP00000260197 ENSCAFP00000017344 1.1659756100193193 WBGene00003806.1 ENSCAFP00000053904 1.1458763815202004 ENSCAFP00000048558 WBGene00013724.1 0.8693032690258004 ENSRNOP00000014377 ENSCAFP00000053904 1.2497712083745642 -ENSCAFP00000048558 ENSRNOP00000016871 0.750765381543786 -ENSCINP00000005198 ENSCAFP00000053904 1.6887514905455063 -ENSCAFP00000048558 ENSCINP00000010262 0.7763303207340811 +ENSRNOP00000016871 ENSCAFP00000048558 0.750765381543786 +ENSCAFP00000053904 ENSCINP00000005198 1.6887514905455063 +ENSCINP00000010262 ENSCAFP00000048558 0.7763303207340811 ENSGALP00000060372 ENSCAFP00000053904 1.032440253327753 ENSCAFP00000048558 ENSGALP00000028084 0.7319060730167674 -ENSCAFP00000017344 ENSGALP00000046461 1.2366809018588243 -ENSMODP00000006811 ENSCAFP00000053904 1.1768064885005973 -ENSCAFP00000048558 ENSMODP00000002384 0.7250057434303576 -ENSCAFP00000017344 ENSMODP00000016287 1.0991546578371612 -ENSPTRP00000071151 ENSTNIP00000005325 1.078068617227524 +ENSGALP00000046461 ENSCAFP00000017344 1.2366809018588243 +ENSCAFP00000053904 ENSMODP00000006811 1.1768064885005973 +ENSMODP00000002384 ENSCAFP00000048558 0.7250057434303576 +ENSMODP00000016287 ENSCAFP00000017344 1.0991546578371612 +ENSTNIP00000005325 ENSPTRP00000071151 1.078068617227524 ENSPTRP00000079818 ENSTNIP00000019800 1.0816122924235794 ENSTNIP00000017394 ENSPTRP00000007532 0.8411232457073231 -ENSDARP00000071531 ENSTNIP00000005325 1.1071998554333529 -ENSDARP00000147265 ENSTNIP00000005325 1.080236084220364 -ENSDARP00000154605 ENSTNIP00000005325 1.0793124107836642 -ENSDARP00000110254 ENSTNIP00000019800 0.9783171648990983 +ENSTNIP00000005325 ENSDARP00000071531 1.1071998554333529 +ENSTNIP00000005325 ENSDARP00000147265 1.080236084220364 +ENSTNIP00000005325 ENSDARP00000154605 1.0793124107836642 +ENSTNIP00000019800 ENSDARP00000110254 0.9783171648990983 ENSTNIP00000019800 ENSDARP00000149121 0.8594599323873157 ENSDARP00000129655 ENSTNIP00000017394 0.9153920541003192 -ENSP00000373312 ENSTNIP00000005325 1.0760130248575053 +ENSTNIP00000005325 ENSP00000373312 1.0760130248575053 ENSP00000340836 ENSTNIP00000019800 1.0832989464755691 -ENSTNIP00000017394 ENSP00000260197 0.8413995792976301 -WBGene00003806.1 ENSTNIP00000005325 0.9341684397011618 -WBGene00013724.1 ENSTNIP00000019800 1.0783142114156974 -ENSRNOP00000014377 ENSTNIP00000005325 1.0277296796262056 +ENSP00000260197 ENSTNIP00000017394 0.8413995792976301 +ENSTNIP00000005325 WBGene00003806.1 0.9341684397011618 +ENSTNIP00000019800 WBGene00013724.1 1.0783142114156974 +ENSTNIP00000005325 ENSRNOP00000014377 1.0277296796262056 ENSRNOP00000016871 ENSTNIP00000019800 0.9726176544674653 -ENSCINP00000005198 ENSTNIP00000005325 1.5030185275774275 +ENSTNIP00000005325 ENSCINP00000005198 1.5030185275774275 ENSCINP00000010262 ENSTNIP00000019800 1.0308419087795246 -ENSTNIP00000017394 ENSCINP00000024362 0.4718462562136554 -ENSGALP00000060372 ENSTNIP00000005325 0.9808125708283421 -ENSGALP00000028084 ENSTNIP00000019800 1.022483154403245 +ENSCINP00000024362 ENSTNIP00000017394 0.4718462562136554 +ENSTNIP00000005325 ENSGALP00000060372 0.9808125708283421 +ENSTNIP00000019800 ENSGALP00000028084 1.022483154403245 ENSTNIP00000017394 ENSGALP00000046461 0.998411869291212 -ENSMODP00000006811 ENSTNIP00000005325 1.1315750573240722 +ENSTNIP00000005325 ENSMODP00000006811 1.1315750573240722 ENSMODP00000002384 ENSTNIP00000019800 1.0525305957202595 ENSTNIP00000017394 ENSMODP00000016287 0.816761291983043 ENSDARP00000071531 ENSPTRP00000071151 1.0948975951481827 ENSPTRP00000071151 ENSDARP00000147265 1.0690571934317779 ENSDARP00000154605 ENSPTRP00000071151 1.0688977991879383 -ENSDARP00000110254 ENSPTRP00000079818 1.0342390860229558 +ENSPTRP00000079818 ENSDARP00000110254 1.0342390860229558 ENSPTRP00000079818 ENSDARP00000149121 0.9106986195805375 ENSDARP00000129655 ENSPTRP00000007532 0.8719045883246118 -ENSP00000373312 ENSPTRP00000071151 0.9949301160533697 +ENSPTRP00000071151 ENSP00000373312 0.9949301160533697 ENSPTRP00000079818 ENSP00000340836 0.979518244878341 -ENSPTRP00000007532 ENSP00000260197 1.0256097745197357 -WBGene00003806.1 ENSPTRP00000071151 0.8995437289862245 -WBGene00013724.1 ENSPTRP00000079818 1.1128612504715538 +ENSP00000260197 ENSPTRP00000007532 1.0256097745197357 +ENSPTRP00000071151 WBGene00003806.1 0.8995437289862245 +ENSPTRP00000079818 WBGene00013724.1 1.1128612504715538 ENSPTRP00000071151 ENSRNOP00000014377 0.9876707502252766 ENSPTRP00000079818 ENSRNOP00000016871 1.0124627007611073 -ENSCINP00000005198 ENSPTRP00000071151 1.4619889679838727 +ENSPTRP00000071151 ENSCINP00000005198 1.4619889679838727 ENSCINP00000010262 ENSPTRP00000079818 1.0476340139447413 ENSCINP00000024362 ENSPTRP00000007532 0.4933020456912314 -ENSGALP00000060372 ENSPTRP00000071151 0.8900349329976032 -ENSGALP00000028084 ENSPTRP00000079818 0.9800259324955464 -ENSPTRP00000007532 ENSGALP00000046461 1.13079100088383 +ENSPTRP00000071151 ENSGALP00000060372 0.8900349329976032 +ENSPTRP00000079818 ENSGALP00000028084 0.9800259324955464 +ENSGALP00000046461 ENSPTRP00000007532 1.13079100088383 ENSPTRP00000071151 ENSMODP00000006811 0.9749376024616611 -ENSMODP00000002384 ENSPTRP00000079818 1.0286917397835451 -ENSPTRP00000007532 ENSMODP00000016287 0.9969408410146324 +ENSPTRP00000079818 ENSMODP00000002384 1.0286917397835451 +ENSMODP00000016287 ENSPTRP00000007532 0.9969408410146324 ENSDARP00000071531 ENSDARP00000147265 0.9724530402585306 -ENSDARP00000071531 ENSDARP00000154605 0.9724530402585306 +ENSDARP00000154605 ENSDARP00000071531 0.9724530402585306 ENSDARP00000154605 ENSDARP00000147265 1.0056169849533259 ENSDARP00000110254 ENSDARP00000149121 0.8209655168956405 ENSDARP00000071531 ENSP00000373312 1.092309927325126 -ENSP00000373312 ENSDARP00000147265 1.0668462539159997 -ENSDARP00000110254 ENSP00000340836 1.03565166616558 -ENSDARP00000129655 ENSP00000260197 0.8729177743346621 +ENSDARP00000147265 ENSP00000373312 1.0668462539159997 +ENSP00000340836 ENSDARP00000110254 1.03565166616558 +ENSP00000260197 ENSDARP00000129655 0.8729177743346621 ENSDARP00000071531 WBGene00003806.1 0.9524828140186127 -ENSDARP00000110254 WBGene00013724.1 1.061887284814649 +WBGene00013724.1 ENSDARP00000110254 1.061887284814649 ENSDARP00000071531 ENSRNOP00000014377 1.058713802727288 ENSDARP00000147265 ENSRNOP00000014377 1.0302014701833606 -ENSDARP00000110254 ENSRNOP00000016871 0.9421452136171529 +ENSRNOP00000016871 ENSDARP00000110254 0.9421452136171529 ENSDARP00000071531 ENSCINP00000005198 1.5381718365133896 -ENSCINP00000005198 ENSDARP00000147265 1.495029099310047 -ENSDARP00000110254 ENSCINP00000010262 0.993006198131263 -ENSDARP00000129655 ENSCINP00000024362 0.4729883042736134 +ENSDARP00000147265 ENSCINP00000005198 1.495029099310047 +ENSCINP00000010262 ENSDARP00000110254 0.993006198131263 +ENSCINP00000024362 ENSDARP00000129655 0.4729883042736134 ENSDARP00000071531 ENSGALP00000060372 0.994064929295005 ENSGALP00000028084 ENSDARP00000110254 0.9847113779623486 ENSDARP00000129655 ENSGALP00000046461 1.0222281124094135 ENSDARP00000071531 ENSMODP00000006811 1.1474514789769603 ENSDARP00000147265 ENSMODP00000006811 1.1165699720173847 -ENSDARP00000110254 ENSMODP00000002384 1.0133686824287944 +ENSMODP00000002384 ENSDARP00000110254 1.0133686824287944 ENSDARP00000129655 ENSMODP00000016287 0.8407101876638388 -ENSP00000373312 ENSDARP00000154605 1.0666866419689747 +ENSDARP00000154605 ENSP00000373312 1.0666866419689747 ENSP00000340836 ENSDARP00000149121 0.9119424661952323 -ENSP00000373312 WBGene00003806.1 0.8992587618133254 -WBGene00013724.1 ENSP00000340836 1.1133139966849854 -ENSP00000373312 ENSRNOP00000014377 0.9860799449831307 -ENSP00000340836 ENSRNOP00000016871 1.0141205592757112 +WBGene00003806.1 ENSP00000373312 0.8992587618133254 +ENSP00000340836 WBGene00013724.1 1.1133139966849854 +ENSRNOP00000014377 ENSP00000373312 0.9860799449831307 +ENSRNOP00000016871 ENSP00000340836 1.0141205592757112 ENSP00000373312 ENSCINP00000005198 1.4611709465315714 ENSCINP00000010262 ENSP00000340836 1.0480563573199848 -ENSP00000373312 ENSGALP00000060372 0.8882376517946002 -ENSGALP00000028084 ENSP00000340836 0.9823721009325256 -ENSGALP00000046461 ENSP00000260197 1.1306740611776718 +ENSGALP00000060372 ENSP00000373312 0.8882376517946002 +ENSP00000340836 ENSGALP00000028084 0.9823721009325256 +ENSP00000260197 ENSGALP00000046461 1.1306740611776718 ENSP00000373312 ENSMODP00000006811 0.9734326265560835 ENSMODP00000002384 ENSP00000340836 1.0303884611821357 -ENSMODP00000016287 ENSP00000260197 0.9968177106624055 -WBGene00003806.1 ENSDARP00000147265 0.9035585575356653 -WBGene00003806.1 ENSDARP00000154605 0.9035585575356653 +ENSP00000260197 ENSMODP00000016287 0.9968177106624055 +ENSDARP00000147265 WBGene00003806.1 0.9035585575356653 +ENSDARP00000154605 WBGene00003806.1 0.9035585575356653 WBGene00013724.1 ENSDARP00000149121 0.8867247529323182 WBGene00003806.1 ENSRNOP00000014377 0.924003520201405 -WBGene00013724.1 ENSRNOP00000016871 1.0878197819809396 -ENSCINP00000005198 WBGene00003806.1 0.9330541938292204 -WBGene00013724.1 ENSCINP00000010262 1.0742379802460436 +ENSRNOP00000016871 WBGene00013724.1 1.0878197819809396 +WBGene00003806.1 ENSCINP00000005198 0.9330541938292204 +ENSCINP00000010262 WBGene00013724.1 1.0742379802460436 ENSGALP00000028084 WBGene00013724.1 1.1163656112128608 WBGene00003806.1 ENSMODP00000006811 0.9260965348362314 -WBGene00013724.1 ENSMODP00000002384 1.0848712552404072 +ENSMODP00000002384 WBGene00013724.1 1.0848712552404072 ENSDARP00000154605 ENSRNOP00000014377 1.0286633969224124 ENSRNOP00000016871 ENSDARP00000149121 0.8303315017735424 -ENSCINP00000005198 ENSRNOP00000014377 1.2020864960788595 +ENSRNOP00000014377 ENSCINP00000005198 1.2020864960788595 ENSCINP00000010262 ENSRNOP00000016871 0.7998840304515645 ENSGALP00000060372 ENSRNOP00000014377 0.9656107168863438 -ENSGALP00000028084 ENSRNOP00000016871 1.0358908406122709 +ENSRNOP00000016871 ENSGALP00000028084 1.0358908406122709 ENSRNOP00000014377 ENSMODP00000006811 1.014568295990869 -ENSMODP00000002384 ENSRNOP00000016871 0.9858168713252738 -ENSCAFP00000017344 ENSCINP00000024362 0.5392752828930565 -ENSCINP00000005198 ENSDARP00000154605 1.491300131871246 +ENSRNOP00000016871 ENSMODP00000002384 0.9858168713252738 +ENSCINP00000024362 ENSCAFP00000017344 0.5392752828930565 +ENSDARP00000154605 ENSCINP00000005198 1.491300131871246 ENSCINP00000010262 ENSDARP00000149121 0.8499085703153215 ENSCINP00000024362 ENSP00000260197 0.4937093636879676 -ENSCINP00000005198 ENSGALP00000060372 1.388829513749228 -ENSGALP00000028084 ENSCINP00000010262 1.0053941211274267 +ENSGALP00000060372 ENSCINP00000005198 1.388829513749228 +ENSCINP00000010262 ENSGALP00000028084 1.0053941211274267 ENSCINP00000024362 ENSGALP00000046461 0.6139352479277681 -ENSCINP00000005198 ENSMODP00000006811 1.512341563219763 +ENSMODP00000006811 ENSCINP00000005198 1.512341563219763 ENSCINP00000010262 ENSMODP00000002384 1.01157228347777 ENSCINP00000024362 ENSMODP00000016287 0.4844878180487609 ENSGALP00000060372 ENSMUSP00000032440 0.9226253791108336 ENSGALP00000060372 ENSDARP00000147265 0.9787006097925798 -ENSGALP00000060372 ENSDARP00000154605 0.9787006097925798 +ENSDARP00000154605 ENSGALP00000060372 0.9787006097925798 ENSGALP00000028084 ENSDARP00000149121 0.8508452087136668 ENSGALP00000060372 WBGene00003806.1 0.8967195494012699 ENSGALP00000060372 ENSMODP00000006811 0.9202902491145213 -ENSGALP00000028084 ENSMODP00000002384 0.966092055738595 +ENSMODP00000002384 ENSGALP00000028084 0.966092055738595 ENSGALP00000046461 ENSMODP00000016287 1.115319260624795 ENSDARP00000154605 ENSMODP00000006811 1.115264423964748 ENSMODP00000002384 ENSDARP00000149121 0.891019663837538 diff --git a/tests/samples/orthohmm_working_res/orthohmm_edges_clustered.txt b/tests/samples/orthohmm_working_res/orthohmm_edges_clustered.txt index c59f9f3..c4e5425 100644 --- a/tests/samples/orthohmm_working_res/orthohmm_edges_clustered.txt +++ b/tests/samples/orthohmm_working_res/orthohmm_edges_clustered.txt @@ -1,4 +1,4 @@ ENSMUSP00000032440 ENSCAFP00000053904 ENSTNIP00000005325 ENSPTRP00000071151 ENSDARP00000071531 ENSDARP00000147265 ENSDARP00000154605 ENSP00000373312 WBGene00003806.1 ENSRNOP00000014377 ENSCINP00000005198 ENSMODP00000006811 ENSGALP00000060372 -ENSTNIP00000019800 ENSMUSP00000025631 ENSPTRP00000079818 ENSDARP00000110254 ENSDARP00000149121 ENSP00000340836 WBGene00013724.1 ENSRNOP00000016871 ENSCINP00000010262 ENSGALP00000028084 ENSMODP00000002384 ENSCAFP00000048558 -ENSCAFP00000017344 ENSMUSP00000058613 ENSTNIP00000017394 ENSPTRP00000007532 ENSDARP00000129655 ENSP00000260197 ENSCINP00000024362 ENSGALP00000046461 ENSMODP00000016287 +ENSMUSP00000025631 ENSTNIP00000019800 ENSPTRP00000079818 ENSDARP00000110254 ENSDARP00000149121 ENSP00000340836 WBGene00013724.1 ENSRNOP00000016871 ENSCINP00000010262 ENSGALP00000028084 ENSMODP00000002384 ENSCAFP00000048558 +ENSMUSP00000058613 ENSCAFP00000017344 ENSTNIP00000017394 ENSPTRP00000007532 ENSDARP00000129655 ENSP00000260197 ENSCINP00000024362 ENSGALP00000046461 ENSMODP00000016287 ENSMUSP00000086311 ENSMUSP00000086314 ENSRNOP00000065522 diff --git a/tests/unit/test_args_parsing.py b/tests/unit/test_args_parsing.py index bc9e5f0..ff881de 100644 --- a/tests/unit/test_args_parsing.py +++ b/tests/unit/test_args_parsing.py @@ -3,7 +3,11 @@ from pathlib import Path from orthohmm.args_processing import process_args -from orthohmm.helpers import StartStep, StopStep +from orthohmm.helpers import ( + StartStep, + StopStep, + SubstitutionMatrix, +) here = Path(__file__) @@ -21,6 +25,7 @@ def args(): inflation_value=1.5, start=None, stop=None, + substitution_matrix=SubstitutionMatrix.blosum62 ) return Namespace(**kwargs) @@ -66,6 +71,11 @@ def test_process_args_search_res_start(self, args): res = process_args(args) assert res["start"] is StartStep.search_res + def test_process_args_substitution_matrix_default(self, args): + args.substitution_matrix = "BLOSUM62" + res = process_args(args) + assert res["substitution_matrix"] is SubstitutionMatrix.blosum62 + def test_process_args_default_stop(self, args): args.stop = None res = process_args(args) @@ -98,5 +108,6 @@ def test_process_args_expected_keywords(self, args): "inflation_value", "start", "stop", + "substitution_matrix", ] assert sorted(res.keys()) == sorted(expected_keys)