added argument enabling users to specify the substitution matrix bein…

…g used
JLSteenwyk · Aug 23, 2024 · 538cbfd · 538cbfd
1 parent 6185b8e
commit 538cbfd
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Showing 131 changed files with 403 additions and 341 deletions.
diff --git 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
@@ -1,4 +1,3 @@
-import itertools
 import multiprocessing
 import subprocess
 from typing import List

diff --git a/orthohmm/helpers.py b/orthohmm/helpers.py
@@ -23,21 +23,34 @@ 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,
     output_directory: str,
     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
@@ -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
@@ -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>                         path to phmmer from HMMER suite
                                                     (default: phmmer)
 
+        -x, --substitution_matrix <subs. matrix>    substitution matrix to use for
+                                                    residue probabilities
+                                                    (default: BLOSUM62)
+
         -c, --cpu <integer>                         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
@@ -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
@@ -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/...is_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/...is_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/...abditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/...abditis_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/...enorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/...enorhabditis_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/.../Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/.../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/...aenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/...aenorhabditis_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/...Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/...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/...tis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/...tis_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/...Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/...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]