From ae122bce9308d0c86f9efaab0c4d6ded399ee087 Mon Sep 17 00:00:00 2001 From: JLSteenwyk Date: Sun, 25 Aug 2024 11:06:56 -0700 Subject: [PATCH] added support for different substitution matrices --- orthohmm/parser.py | 2 +- orthohmm/writer.py | 14 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- ..._elegans.WBcel235.pep.all.fa.phmmerout.txt | 8 +- ...iliaris.CanFam3.1.pep.all.fa.phmmerout.txt | 8 +- ...a_intestinalis.KH.pep.all.fa.phmmerout.txt | 8 +- ...anio_rerio.GRCz11.pep.all.fa.phmmerout.txt | 8 +- ...lus_gallus.GRCg6a.pep.all.fa.phmmerout.txt | 8 +- ...mo_sapiens.GRCh38.pep.all.fa.phmmerout.txt | 8 +- ...omestica.ASM229v1.pep.all.fa.phmmerout.txt | 8 +- ...s_musculus.GRCm38.pep.all.fa.phmmerout.txt | 8 +- ...dytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt | 8 +- ...rvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt | 8 +- ...iridis.TETRAODON8.pep.all.fa.phmmerout.txt | 8 +- .../orthohmm_working_res/orthohmm_edges.txt | 186 +++++++++--------- .../orthohmm_edges_clustered.txt | 6 +- 125 files changed, 588 insertions(+), 588 deletions(-) diff --git a/orthohmm/parser.py b/orthohmm/parser.py index 1360f07..59ea198 100644 --- a/orthohmm/parser.py +++ b/orthohmm/parser.py @@ -196,7 +196,7 @@ def create_parser() -> ArgumentParser: metavar="output_directory" ) - substitution_matrix_choices = [step.value for step in SubstitutionMatrix] + substitution_matrix_choices = [matrix.value for matrix in SubstitutionMatrix] optional.add_argument( "-x", "--substitution_matrix", diff --git a/orthohmm/writer.py b/orthohmm/writer.py index c095e08..0aa933d 100644 --- a/orthohmm/writer.py +++ b/orthohmm/writer.py @@ -38,14 +38,14 @@ def write_user_args( print( textwrap.dedent( f"""\ - ____ _ _ _ _ __ __ __ __ - / __ \ | | | | | | | | \/ | \/ | - | | | |_ __| |_| |__ ___ | |__| | \ / | \ / | - | | | | '__| __| '_ \ / _ \| __ | |\/| | |\/| | - | |__| | | | |_| | | | (_) | | | | | | | | | | - \____/|_| \__|_| |_|\___/|_| |_|_| |_|_| |_| + ____ _ _ _ _ __ __ __ __ + / __ \ | | | | | | | | \/ | \/ | + | | | |_ __| |_| |__ ___ | |__| | \ / | \ / | + | | | | '__| __| '_ \ / _ \| __ | |\/| | |\/| | + | |__| | | | |_| | | | (_) | | | | | | | | | | + \____/|_| \__|_| |_|\___/|_| |_|_| |_|_| |_| - Version: {__version__} + Version: {__version__} ------------- | Arguments | 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 e9596a6..2cab11d 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 @@ -7,9 +7,9 @@ WBGene00013724.1 - WBGene00013724.1 - 9.1e-152 489.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 7cb2375..ee57577 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 @@ -7,9 +7,9 @@ ENSCAFP00000048558 - WBGene00013724.1 - 4.3e-60 190.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 87418ae..7ce2f15 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 @@ -7,9 +7,9 @@ ENSCINP00000010262 - WBGene00013724.1 - 4.1e-65 207.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 edc0c92..58895fb 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 @@ -10,9 +10,9 @@ ENSDARP00000149121 - WBGene00013724.1 - 4e-50 159.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 110d34a..7437d0d 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 @@ -7,9 +7,9 @@ ENSGALP00000028084 - WBGene00013724.1 - 1.8e-65 208.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 aad4c37..28a3ce3 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 @@ -7,9 +7,9 @@ ENSP00000340836 - WBGene00013724.1 - 4.7e-68 216.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 0aba790..22b4f69 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 @@ -7,9 +7,9 @@ ENSMODP00000002384 - WBGene00013724.1 - 1.8e-68 218.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 8a5c53c..2679bc5 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 @@ -7,9 +7,9 @@ ENSMUSP00000025631 - WBGene00013724.1 - 3.7e-67 214.7 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 d394401..48be7a5 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 @@ -7,9 +7,9 @@ ENSPTRP00000079818 - WBGene00013724.1 - 4.7e-68 216.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 cbb283b..6cf00b3 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 @@ -8,9 +8,9 @@ ENSRNOP00000016871 - WBGene00013724.1 - 4e-68 217.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 73d799c..d197763 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 @@ -7,9 +7,9 @@ ENSTNIP00000019800 - WBGene00013724.1 - 2.2e-65 208.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 98314ad..92c4680 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 @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSCAFP00000048558 - 1.3e-60 192.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 29dfcd8..930ab9c 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 @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSCAFP00000017344 - 0 5307.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 11e65d7..8e719f0 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 @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSCAFP00000017344 - 1.3e-291 958.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 1f24827..5f29a6d 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 @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSCAFP00000017344 - 0 3406.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 47fb3be..7bfe189 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 @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSCAFP00000017344 - 0 4126.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 bfbf686..730daa4 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 @@ -8,9 +8,9 @@ ENSP00000260197 - ENSCAFP00000017344 - 0 4968.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 c790a7c..ac112e0 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 @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSCAFP00000017344 - 0 4656.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 77a9275..c7ce06f 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 @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSCAFP00000017344 - 0 4829.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 ad399bc..8420262 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 @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSCAFP00000017344 - 0 4983.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 3c7c66f..365e300 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 @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSCAFP00000048558 - 1.4e-125 407.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 b87affb..64620be 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 @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSCAFP00000017344 - 0 3325.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 eea0d32..4e85d71 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 @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSCINP00000010262 - 2.5e-65 207.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 67deade..1656bb6 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 @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSCINP00000024362 - 1.5e-292 961.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 a4b96a2..aa1e386 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 @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSCINP00000024362 - 0 3552.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 3ad6b0b..03c3d82 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 @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSCINP00000024362 - 1.3e-283 932.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 6ccfbf8..70b7b4e 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 @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSCINP00000024362 - 1.3e-293 964.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 7403b51..2a96fd5 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 @@ -8,9 +8,9 @@ ENSP00000260197 - ENSCINP00000024362 - 2.3e-288 947.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 4602977..521365f 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 @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSCINP00000024362 - 3.7e-297 976.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 aadada1..de6a967 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 @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSCINP00000024362 - 5.2e-290 953.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 5e01e71..f379473 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 @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSCINP00000024362 - 4.7e-288 946.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 60edba1..210be06 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 @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSCINP00000010262 - 4.5e-74 236.7 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 c86d28a..c9f460c 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 @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSCINP00000024362 - 1.3e-279 918.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Ciona_intestinalis.KH.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Ciona_intestinalis.KH.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 f49f3cc..eb2ccad 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 @@ -10,9 +10,9 @@ WBGene00013724.1 - ENSDARP00000149121 - 2.2e-51 161.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:22 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 5e853e2..ec3a41e 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 @@ -11,9 +11,9 @@ ENSCAFP00000017344 - ENSDARP00000129655 - 0 3409.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:22 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 a2ed816..7a82c9b 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 @@ -11,9 +11,9 @@ ENSCINP00000024362 - ENSDARP00000129655 - 2e-284 934.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 70f43c3..c68acf6 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 @@ -19,9 +19,9 @@ ENSDARP00000129655 - ENSDARP00000129655 - 0 5322.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:22 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 b3d6800..24db61c 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 @@ -11,9 +11,9 @@ ENSGALP00000046461 - ENSDARP00000129655 - 0 3423.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 9cbc185..6a157e1 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 @@ -11,9 +11,9 @@ ENSP00000260197 - ENSDARP00000129655 - 0 3439.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:22 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 56c4367..6c48bf2 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 @@ -11,9 +11,9 @@ ENSMODP00000016287 - ENSDARP00000129655 - 0 3474.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 08deb0f..98b5460 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 @@ -11,9 +11,9 @@ ENSMUSP00000058613 - ENSDARP00000129655 - 0 3430.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:22 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 c1b7d01..7c41228 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 @@ -11,9 +11,9 @@ ENSPTRP00000007532 - ENSDARP00000129655 - 0 3439.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:22 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 6f21135..14e4cee 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 @@ -13,9 +13,9 @@ ENSRNOP00000016871 - ENSDARP00000149121 - 6.6e-104 333.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:22 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 b8c2761..9b59c7c 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 @@ -11,9 +11,9 @@ ENSTNIP00000017394 - ENSDARP00000129655 - 0 4009.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Danio_rerio.GRCz11.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Danio_rerio.GRCz11.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:22 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 30ac8fb..796ac5e 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 @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSGALP00000028084 - 3.7e-66 210.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 fa915df..85f3b46 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 @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSGALP00000046461 - 0 4127.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 e01a8ff..2bfed1d 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 @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSGALP00000046461 - 1.2e-290 954.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:24 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 2025bf1..322d692 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 @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSGALP00000046461 - 0 3421.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 130c517..9e35bf3 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 @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSGALP00000046461 - 0 5310.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:24 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 b13cfc4..bf2ae32 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 @@ -8,9 +8,9 @@ ENSP00000260197 - ENSGALP00000046461 - 0 4163.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:24 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 35905f8..6da83da 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 @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSGALP00000046461 - 0 4256.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:24 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 51a4da0..e264dd2 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 @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSGALP00000046461 - 0 4101.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 77f3ce3..5516298 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 @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSGALP00000046461 - 0 4174.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 1c3a9a9..be7280b 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 @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSGALP00000028084 - 4.1e-141 457.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:24 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 2736e5d..69f48b9 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 @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSGALP00000046461 - 0 3326.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Gallus_gallus.GRCg6a.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 86823b6..824c1e8 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 @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSP00000340836 - 1e-68 218.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 cee4069..bb77db1 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 @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSP00000260197 - 0 4969.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 b7339d5..bc70cc3 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 @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSP00000260197 - 2.3e-288 947.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 20920dd..29e2829 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 @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSP00000260197 - 0 3436.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 1443b5d..ea2e861 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 @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSP00000260197 - 0 4163.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 4045386..8f62524 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 @@ -8,9 +8,9 @@ ENSP00000260197 - ENSP00000260197 - 0 5330.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 54a544e..505ba47 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 @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSP00000260197 - 0 4737.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 6af8234..9ce21ba 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 @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSP00000260197 - 0 4997.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 f16154e..8516fc4 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 @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSP00000260197 - 0 5306.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 d77885a..8cb614f 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 @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSP00000340836 - 1.1e-145 470.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 7b50633..d80325c 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 @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSP00000260197 - 0 3327.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Homo_sapiens.GRCh38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:46 2024 +# Date: Sun Aug 25 08:57:23 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 65a3d53..5cd4dcd 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 @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSMODP00000002384 - 5.2e-69 219.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 59fb12b..e7490f6 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 @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSMODP00000016287 - 0 4656.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 ffd6970..54af773 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 @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSMODP00000016287 - 1.3e-288 947.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 4dd4787..06af324 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 @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSMODP00000016287 - 0 3471.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 b04d5f3..5cac339 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 @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSMODP00000016287 - 0 4255.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 5f370ec..fbb7975 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 @@ -8,9 +8,9 @@ ENSP00000260197 - ENSMODP00000016287 - 0 4737.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 1e524d8..9875d6e 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 @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSMODP00000016287 - 0 5338.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 f7302ca..6ed2ef0 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 @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSMODP00000016287 - 0 4649.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:24 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 97b9b3a..bab5fb4 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 @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSMODP00000016287 - 0 4745.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 0eb546d..c34a43a 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 @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSMODP00000002384 - 3.7e-145 468.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 eaa7f34..095b7a6 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 @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSMODP00000016287 - 0 3367.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Monodelphis_domestica.ASM229v1.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:48 2024 +# Date: Sun Aug 25 08:57:25 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 69fdbd8..d7852dc 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 @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSMUSP00000025631 - 4.9e-68 215.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:20 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 36641ad..8c1a691 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 @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSMUSP00000058613 - 0 4829.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:20 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 39e4819..3b77761 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 @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSMUSP00000058613 - 9.1e-293 961.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 93439e3..a22ff88 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 @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSMUSP00000058613 - 0 3427.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:20 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 13a3ea0..5f489d0 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 @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSMUSP00000058613 - 0 4100.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 70bf269..ae71488 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 @@ -8,9 +8,9 @@ ENSP00000260197 - ENSMUSP00000058613 - 0 4997.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:20 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 f5d3f8a..12c30f8 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 @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSMUSP00000058613 - 0 4649.4 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 61b256a..62c56ad 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 @@ -12,9 +12,9 @@ ENSMUSP00000058613 - ENSMUSP00000058613 - 0 5320.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:20 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 27123d4..b18e63f 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 @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSMUSP00000058613 - 0 5013.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:20 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 6f8d151..77d8fa6 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 @@ -10,9 +10,9 @@ ENSRNOP00000065522 - ENSMUSP00000086314 - 7.7e-256 838.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:20 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 9afab2f..ce81359 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 @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSMUSP00000058613 - 0 3345.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Mus_musculus.GRCm38.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Mus_musculus.GRCm38.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:20 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 745ed1a..3d73620 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 @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSPTRP00000079818 - 1e-68 218.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 3bf1ef9..40f49f7 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 @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSPTRP00000007532 - 0 4983.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 6a62a76..a4f76e2 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 @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSPTRP00000007532 - 2.7e-288 947.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 303eaf1..7795b71 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 @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSPTRP00000007532 - 0 3436.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 fc31ea5..b5779fd 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 @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSPTRP00000007532 - 0 4173.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 3086aed..84e600d 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 @@ -8,9 +8,9 @@ ENSP00000260197 - ENSPTRP00000007532 - 0 5306.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 e2d61c6..105c444 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 @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSPTRP00000007532 - 0 4745.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 6b7ed43..2c4fcaa 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 @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSPTRP00000007532 - 0 5013.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 522cd87..b8ce30b 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 @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSPTRP00000007532 - 0 5329.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 fdc929f..ed96ac2 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 @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSPTRP00000079818 - 1.1e-145 470.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 621fa6c..e003dbc 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 @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSPTRP00000007532 - 0 3331.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 ab8feee..ebaa68b 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 @@ -8,9 +8,9 @@ WBGene00013724.1 - ENSRNOP00000016871 - 6.5e-69 218.7 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 1ff96e8..18f972e 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 @@ -8,9 +8,9 @@ ENSCAFP00000048558 - ENSRNOP00000016871 - 2.7e-126 406.8 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 85c6815..e9112ce 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 @@ -8,9 +8,9 @@ ENSCINP00000010262 - ENSRNOP00000016871 - 1.6e-74 237.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 bec3a5d..298c799 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 @@ -13,9 +13,9 @@ ENSDARP00000149121 - ENSRNOP00000016871 - 1.9e-103 333.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 cb8b2ff..fbce6ae 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 @@ -8,9 +8,9 @@ ENSGALP00000028084 - ENSRNOP00000016871 - 9.8e-142 457.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 c3d054f..4e137ea 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 @@ -8,9 +8,9 @@ ENSP00000340836 - ENSRNOP00000016871 - 8e-146 470.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 4791977..1fe4fcb 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 @@ -8,9 +8,9 @@ ENSMODP00000002384 - ENSRNOP00000016871 - 2.3e-145 469.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:24 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 d2f5a64..1ca36fb 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 @@ -10,9 +10,9 @@ ENSMUSP00000086311 - ENSRNOP00000065522 - 1.9e-255 836.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 f4416d4..00e8401 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 @@ -8,9 +8,9 @@ ENSPTRP00000079818 - ENSRNOP00000016871 - 8e-146 470.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 d19f700..8762d69 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 @@ -11,9 +11,9 @@ ENSRNOP00000065522 - ENSRNOP00000065522 - 0 1213.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 cbd5cdd..c0fac8a 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 @@ -8,9 +8,9 @@ ENSTNIP00000019800 - ENSRNOP00000016871 - 3.1e-130 419.6 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:47 2024 +# Date: Sun Aug 25 08:57:23 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 2757c93..f365639 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 @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSTNIP00000019800 - 6.1e-66 209.0 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:21 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 a1687c1..8a6bf51 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 @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSTNIP00000017394 - 0 3329.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 e4810a8..953221a 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 @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSTNIP00000017394 - 4.9e-284 933.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 2279138..293a38c 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 @@ -11,9 +11,9 @@ ENSDARP00000129655 - ENSTNIP00000017394 - 0 4011.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:21 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 0333a1f..512f7e7 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 @@ -8,9 +8,9 @@ ENSGALP00000046461 - ENSTNIP00000017394 - 0 3328.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 41192ed..9dac765 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 @@ -8,9 +8,9 @@ ENSP00000260197 - ENSTNIP00000017394 - 0 3332.1 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:21 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 8f3f78f..27be9dd 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 @@ -8,9 +8,9 @@ ENSMODP00000016287 - ENSTNIP00000017394 - 0 3370.7 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:22 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 0fee573..3b183eb 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 @@ -8,9 +8,9 @@ ENSMUSP00000058613 - ENSTNIP00000017394 - 0 3349.3 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:44 2024 +# Date: Sun Aug 25 08:57:21 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 05c428a..478b9d3 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 @@ -8,9 +8,9 @@ ENSPTRP00000007532 - ENSTNIP00000017394 - 0 3336.2 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:21 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 320f3e7..3c5b295 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 @@ -8,9 +8,9 @@ ENSRNOP00000016871 - ENSTNIP00000019800 - 5e-130 419.5 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa +# Option settings: phmmer --tblout ./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 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:21 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 906009b..13338f3 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 @@ -8,9 +8,9 @@ ENSTNIP00000017394 - ENSTNIP00000017394 - 0 5341.9 # Program: phmmer # Version: 3.3.1 (Jul 2020) # 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 --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 +# Query file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa +# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Tetraodon_nigroviridis.TETRAODON8.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa # Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli -# Date: Fri Aug 23 14:08:45 2024 +# Date: Sun Aug 25 08:57:21 2024 # [ok] diff --git a/tests/samples/orthohmm_working_res/orthohmm_edges.txt b/tests/samples/orthohmm_working_res/orthohmm_edges.txt index 0e77408..6d591bb 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 -ENSMUSP00000058613 ENSCAFP00000017344 1.1191809742240841 +ENSMUSP00000086314 ENSMUSP00000086311 0.9452235456218643 +ENSCAFP00000053904 ENSMUSP00000032440 1.1765339326216484 +ENSCAFP00000017344 ENSMUSP00000058613 1.1191809742240841 ENSTNIP00000005325 ENSMUSP00000032440 1.1230455740952423 ENSMUSP00000025631 ENSTNIP00000019800 1.0573543116888735 ENSMUSP00000058613 ENSTNIP00000017394 0.8204945552781063 ENSPTRP00000071151 ENSMUSP00000032440 0.9750143971399228 -ENSPTRP00000079818 ENSMUSP00000025631 0.9947457998525575 +ENSMUSP00000025631 ENSPTRP00000079818 0.9947457998525575 ENSMUSP00000058613 ENSPTRP00000007532 1.0305438528225042 ENSDARP00000071531 ENSMUSP00000032440 1.1405390347688653 -ENSDARP00000147265 ENSMUSP00000032440 1.109983290000416 +ENSMUSP00000032440 ENSDARP00000147265 1.109983290000416 ENSDARP00000154605 ENSMUSP00000032440 1.1083231295307774 -ENSMUSP00000025631 ENSDARP00000110254 1.014393194490703 -ENSMUSP00000025631 ENSDARP00000149121 0.8935016279742156 -ENSDARP00000129655 ENSMUSP00000058613 0.8464014718555611 -ENSMUSP00000032440 ENSP00000373312 0.9739080572466866 -ENSP00000340836 ENSMUSP00000025631 0.996854926953224 -ENSP00000260197 ENSMUSP00000058613 1.029618128104977 -ENSMUSP00000032440 WBGene00003806.1 0.9330346205728083 +ENSDARP00000110254 ENSMUSP00000025631 1.014393194490703 +ENSDARP00000149121 ENSMUSP00000025631 0.8935016279742156 +ENSMUSP00000058613 ENSDARP00000129655 0.8464014718555611 +ENSP00000373312 ENSMUSP00000032440 0.9739080572466866 +ENSMUSP00000025631 ENSP00000340836 0.996854926953224 +ENSMUSP00000058613 ENSP00000260197 1.029618128104977 +WBGene00003806.1 ENSMUSP00000032440 0.9330346205728083 ENSMUSP00000025631 WBGene00013724.1 1.078616751331466 -ENSMUSP00000032440 ENSRNOP00000014377 1.1575744132634167 +ENSRNOP00000014377 ENSMUSP00000032440 1.1575744132634167 ENSRNOP00000016871 ENSMUSP00000025631 1.118452164541046 -ENSRNOP00000065522 ENSMUSP00000086314 0.724492027798829 -ENSMUSP00000032440 ENSCINP00000005198 1.524489076894231 -ENSCINP00000010262 ENSMUSP00000025631 0.998945905307546 +ENSMUSP00000086314 ENSRNOP00000065522 0.724492027798829 +ENSCINP00000005198 ENSMUSP00000032440 1.524489076894231 +ENSMUSP00000025631 ENSCINP00000010262 0.998945905307546 ENSCINP00000024362 ENSMUSP00000058613 0.4807572315142691 ENSMUSP00000025631 ENSGALP00000028084 0.981655351115904 ENSMUSP00000058613 ENSGALP00000046461 1.0971675453571852 -ENSMUSP00000032440 ENSMODP00000006811 1.035122951917207 +ENSMODP00000006811 ENSMUSP00000032440 1.035122951917207 ENSMODP00000002384 ENSMUSP00000025631 1.001174747698835 ENSMUSP00000058613 ENSMODP00000016287 0.9642127408498951 -ENSCAFP00000048558 ENSMUSP00000025631 0.7048020506658835 -ENSTNIP00000005325 ENSCAFP00000053904 1.29041322599113 -ENSCAFP00000048558 ENSTNIP00000019800 0.773726752517809 -ENSTNIP00000017394 ENSCAFP00000017344 0.9375675734980686 +ENSMUSP00000025631 ENSCAFP00000048558 0.7048020506658835 +ENSCAFP00000053904 ENSTNIP00000005325 1.29041322599113 +ENSTNIP00000019800 ENSCAFP00000048558 0.773726752517809 +ENSCAFP00000017344 ENSTNIP00000017394 0.9375675734980686 ENSPTRP00000071151 ENSCAFP00000053904 1.1117442428910387 ENSPTRP00000079818 ENSCAFP00000048558 0.7222433706443235 ENSCAFP00000017344 ENSPTRP00000007532 1.1666255159560786 -ENSDARP00000147265 ENSCAFP00000053904 1.2662879716451452 +ENSCAFP00000053904 ENSDARP00000147265 1.2662879716451452 ENSDARP00000154605 ENSCAFP00000053904 1.264976532704249 ENSDARP00000071531 ENSCAFP00000053904 1.2961637997082234 -ENSCAFP00000048558 ENSDARP00000110254 0.7495847510861663 -ENSDARP00000129655 ENSCAFP00000017344 0.9559051251977784 -ENSCAFP00000053904 ENSP00000373312 1.110881900680476 +ENSDARP00000110254 ENSCAFP00000048558 0.7495847510861663 +ENSCAFP00000017344 ENSDARP00000129655 0.9559051251977784 +ENSP00000373312 ENSCAFP00000053904 1.110881900680476 ENSP00000340836 ENSCAFP00000048558 0.7239183668098337 -ENSP00000260197 ENSCAFP00000017344 1.1659756100193193 +ENSCAFP00000017344 ENSP00000260197 1.1659756100193193 WBGene00003806.1 ENSCAFP00000053904 1.1458763815202004 -ENSCAFP00000048558 WBGene00013724.1 0.8693032690258004 +WBGene00013724.1 ENSCAFP00000048558 0.8693032690258004 ENSRNOP00000014377 ENSCAFP00000053904 1.2497712083745642 ENSRNOP00000016871 ENSCAFP00000048558 0.750765381543786 -ENSCAFP00000053904 ENSCINP00000005198 1.6887514905455063 +ENSCINP00000005198 ENSCAFP00000053904 1.6887514905455063 ENSCINP00000010262 ENSCAFP00000048558 0.7763303207340811 ENSGALP00000060372 ENSCAFP00000053904 1.032440253327753 -ENSCAFP00000048558 ENSGALP00000028084 0.7319060730167674 -ENSGALP00000046461 ENSCAFP00000017344 1.2366809018588243 +ENSGALP00000028084 ENSCAFP00000048558 0.7319060730167674 +ENSCAFP00000017344 ENSGALP00000046461 1.2366809018588243 ENSCAFP00000053904 ENSMODP00000006811 1.1768064885005973 ENSMODP00000002384 ENSCAFP00000048558 0.7250057434303576 -ENSMODP00000016287 ENSCAFP00000017344 1.0991546578371612 -ENSTNIP00000005325 ENSPTRP00000071151 1.078068617227524 +ENSCAFP00000017344 ENSMODP00000016287 1.0991546578371612 +ENSPTRP00000071151 ENSTNIP00000005325 1.078068617227524 ENSPTRP00000079818 ENSTNIP00000019800 1.0816122924235794 -ENSTNIP00000017394 ENSPTRP00000007532 0.8411232457073231 -ENSTNIP00000005325 ENSDARP00000071531 1.1071998554333529 +ENSPTRP00000007532 ENSTNIP00000017394 0.8411232457073231 +ENSDARP00000071531 ENSTNIP00000005325 1.1071998554333529 ENSTNIP00000005325 ENSDARP00000147265 1.080236084220364 -ENSTNIP00000005325 ENSDARP00000154605 1.0793124107836642 -ENSTNIP00000019800 ENSDARP00000110254 0.9783171648990983 -ENSTNIP00000019800 ENSDARP00000149121 0.8594599323873157 +ENSDARP00000154605 ENSTNIP00000005325 1.0793124107836642 +ENSDARP00000110254 ENSTNIP00000019800 0.9783171648990983 +ENSDARP00000149121 ENSTNIP00000019800 0.8594599323873157 ENSDARP00000129655 ENSTNIP00000017394 0.9153920541003192 -ENSTNIP00000005325 ENSP00000373312 1.0760130248575053 +ENSP00000373312 ENSTNIP00000005325 1.0760130248575053 ENSP00000340836 ENSTNIP00000019800 1.0832989464755691 ENSP00000260197 ENSTNIP00000017394 0.8413995792976301 -ENSTNIP00000005325 WBGene00003806.1 0.9341684397011618 -ENSTNIP00000019800 WBGene00013724.1 1.0783142114156974 -ENSTNIP00000005325 ENSRNOP00000014377 1.0277296796262056 +WBGene00003806.1 ENSTNIP00000005325 0.9341684397011618 +WBGene00013724.1 ENSTNIP00000019800 1.0783142114156974 +ENSRNOP00000014377 ENSTNIP00000005325 1.0277296796262056 ENSRNOP00000016871 ENSTNIP00000019800 0.9726176544674653 -ENSTNIP00000005325 ENSCINP00000005198 1.5030185275774275 +ENSCINP00000005198 ENSTNIP00000005325 1.5030185275774275 ENSCINP00000010262 ENSTNIP00000019800 1.0308419087795246 ENSCINP00000024362 ENSTNIP00000017394 0.4718462562136554 -ENSTNIP00000005325 ENSGALP00000060372 0.9808125708283421 -ENSTNIP00000019800 ENSGALP00000028084 1.022483154403245 -ENSTNIP00000017394 ENSGALP00000046461 0.998411869291212 +ENSGALP00000060372 ENSTNIP00000005325 0.9808125708283421 +ENSGALP00000028084 ENSTNIP00000019800 1.022483154403245 +ENSGALP00000046461 ENSTNIP00000017394 0.998411869291212 ENSTNIP00000005325 ENSMODP00000006811 1.1315750573240722 ENSMODP00000002384 ENSTNIP00000019800 1.0525305957202595 -ENSTNIP00000017394 ENSMODP00000016287 0.816761291983043 -ENSDARP00000071531 ENSPTRP00000071151 1.0948975951481827 +ENSMODP00000016287 ENSTNIP00000017394 0.816761291983043 +ENSPTRP00000071151 ENSDARP00000071531 1.0948975951481827 ENSPTRP00000071151 ENSDARP00000147265 1.0690571934317779 -ENSDARP00000154605 ENSPTRP00000071151 1.0688977991879383 -ENSPTRP00000079818 ENSDARP00000110254 1.0342390860229558 -ENSPTRP00000079818 ENSDARP00000149121 0.9106986195805375 +ENSPTRP00000071151 ENSDARP00000154605 1.0688977991879383 +ENSDARP00000110254 ENSPTRP00000079818 1.0342390860229558 +ENSDARP00000149121 ENSPTRP00000079818 0.9106986195805375 ENSDARP00000129655 ENSPTRP00000007532 0.8719045883246118 ENSPTRP00000071151 ENSP00000373312 0.9949301160533697 -ENSPTRP00000079818 ENSP00000340836 0.979518244878341 -ENSP00000260197 ENSPTRP00000007532 1.0256097745197357 +ENSP00000340836 ENSPTRP00000079818 0.979518244878341 +ENSPTRP00000007532 ENSP00000260197 1.0256097745197357 ENSPTRP00000071151 WBGene00003806.1 0.8995437289862245 -ENSPTRP00000079818 WBGene00013724.1 1.1128612504715538 +WBGene00013724.1 ENSPTRP00000079818 1.1128612504715538 ENSPTRP00000071151 ENSRNOP00000014377 0.9876707502252766 -ENSPTRP00000079818 ENSRNOP00000016871 1.0124627007611073 +ENSRNOP00000016871 ENSPTRP00000079818 1.0124627007611073 ENSPTRP00000071151 ENSCINP00000005198 1.4619889679838727 ENSCINP00000010262 ENSPTRP00000079818 1.0476340139447413 ENSCINP00000024362 ENSPTRP00000007532 0.4933020456912314 ENSPTRP00000071151 ENSGALP00000060372 0.8900349329976032 -ENSPTRP00000079818 ENSGALP00000028084 0.9800259324955464 -ENSGALP00000046461 ENSPTRP00000007532 1.13079100088383 +ENSGALP00000028084 ENSPTRP00000079818 0.9800259324955464 +ENSPTRP00000007532 ENSGALP00000046461 1.13079100088383 ENSPTRP00000071151 ENSMODP00000006811 0.9749376024616611 -ENSPTRP00000079818 ENSMODP00000002384 1.0286917397835451 -ENSMODP00000016287 ENSPTRP00000007532 0.9969408410146324 +ENSMODP00000002384 ENSPTRP00000079818 1.0286917397835451 +ENSPTRP00000007532 ENSMODP00000016287 0.9969408410146324 ENSDARP00000071531 ENSDARP00000147265 0.9724530402585306 -ENSDARP00000154605 ENSDARP00000071531 0.9724530402585306 +ENSDARP00000071531 ENSDARP00000154605 0.9724530402585306 ENSDARP00000154605 ENSDARP00000147265 1.0056169849533259 ENSDARP00000110254 ENSDARP00000149121 0.8209655168956405 ENSDARP00000071531 ENSP00000373312 1.092309927325126 -ENSDARP00000147265 ENSP00000373312 1.0668462539159997 -ENSP00000340836 ENSDARP00000110254 1.03565166616558 -ENSP00000260197 ENSDARP00000129655 0.8729177743346621 +ENSP00000373312 ENSDARP00000147265 1.0668462539159997 +ENSDARP00000110254 ENSP00000340836 1.03565166616558 +ENSDARP00000129655 ENSP00000260197 0.8729177743346621 ENSDARP00000071531 WBGene00003806.1 0.9524828140186127 -WBGene00013724.1 ENSDARP00000110254 1.061887284814649 +ENSDARP00000110254 WBGene00013724.1 1.061887284814649 ENSDARP00000071531 ENSRNOP00000014377 1.058713802727288 -ENSDARP00000147265 ENSRNOP00000014377 1.0302014701833606 -ENSRNOP00000016871 ENSDARP00000110254 0.9421452136171529 +ENSRNOP00000014377 ENSDARP00000147265 1.0302014701833606 +ENSDARP00000110254 ENSRNOP00000016871 0.9421452136171529 ENSDARP00000071531 ENSCINP00000005198 1.5381718365133896 -ENSDARP00000147265 ENSCINP00000005198 1.495029099310047 -ENSCINP00000010262 ENSDARP00000110254 0.993006198131263 +ENSCINP00000005198 ENSDARP00000147265 1.495029099310047 +ENSDARP00000110254 ENSCINP00000010262 0.993006198131263 ENSCINP00000024362 ENSDARP00000129655 0.4729883042736134 ENSDARP00000071531 ENSGALP00000060372 0.994064929295005 -ENSGALP00000028084 ENSDARP00000110254 0.9847113779623486 +ENSDARP00000110254 ENSGALP00000028084 0.9847113779623486 ENSDARP00000129655 ENSGALP00000046461 1.0222281124094135 ENSDARP00000071531 ENSMODP00000006811 1.1474514789769603 -ENSDARP00000147265 ENSMODP00000006811 1.1165699720173847 -ENSMODP00000002384 ENSDARP00000110254 1.0133686824287944 +ENSMODP00000006811 ENSDARP00000147265 1.1165699720173847 +ENSDARP00000110254 ENSMODP00000002384 1.0133686824287944 ENSDARP00000129655 ENSMODP00000016287 0.8407101876638388 -ENSDARP00000154605 ENSP00000373312 1.0666866419689747 -ENSP00000340836 ENSDARP00000149121 0.9119424661952323 -WBGene00003806.1 ENSP00000373312 0.8992587618133254 +ENSP00000373312 ENSDARP00000154605 1.0666866419689747 +ENSDARP00000149121 ENSP00000340836 0.9119424661952323 +ENSP00000373312 WBGene00003806.1 0.8992587618133254 ENSP00000340836 WBGene00013724.1 1.1133139966849854 -ENSRNOP00000014377 ENSP00000373312 0.9860799449831307 +ENSP00000373312 ENSRNOP00000014377 0.9860799449831307 ENSRNOP00000016871 ENSP00000340836 1.0141205592757112 ENSP00000373312 ENSCINP00000005198 1.4611709465315714 -ENSCINP00000010262 ENSP00000340836 1.0480563573199848 -ENSGALP00000060372 ENSP00000373312 0.8882376517946002 +ENSP00000340836 ENSCINP00000010262 1.0480563573199848 +ENSP00000373312 ENSGALP00000060372 0.8882376517946002 ENSP00000340836 ENSGALP00000028084 0.9823721009325256 ENSP00000260197 ENSGALP00000046461 1.1306740611776718 ENSP00000373312 ENSMODP00000006811 0.9734326265560835 ENSMODP00000002384 ENSP00000340836 1.0303884611821357 ENSP00000260197 ENSMODP00000016287 0.9968177106624055 -ENSDARP00000147265 WBGene00003806.1 0.9035585575356653 -ENSDARP00000154605 WBGene00003806.1 0.9035585575356653 -WBGene00013724.1 ENSDARP00000149121 0.8867247529323182 +WBGene00003806.1 ENSDARP00000147265 0.9035585575356653 +WBGene00003806.1 ENSDARP00000154605 0.9035585575356653 +ENSDARP00000149121 WBGene00013724.1 0.8867247529323182 WBGene00003806.1 ENSRNOP00000014377 0.924003520201405 ENSRNOP00000016871 WBGene00013724.1 1.0878197819809396 -WBGene00003806.1 ENSCINP00000005198 0.9330541938292204 -ENSCINP00000010262 WBGene00013724.1 1.0742379802460436 -ENSGALP00000028084 WBGene00013724.1 1.1163656112128608 +ENSCINP00000005198 WBGene00003806.1 0.9330541938292204 +WBGene00013724.1 ENSCINP00000010262 1.0742379802460436 +WBGene00013724.1 ENSGALP00000028084 1.1163656112128608 WBGene00003806.1 ENSMODP00000006811 0.9260965348362314 ENSMODP00000002384 WBGene00013724.1 1.0848712552404072 ENSDARP00000154605 ENSRNOP00000014377 1.0286633969224124 ENSRNOP00000016871 ENSDARP00000149121 0.8303315017735424 -ENSRNOP00000014377 ENSCINP00000005198 1.2020864960788595 -ENSCINP00000010262 ENSRNOP00000016871 0.7998840304515645 +ENSCINP00000005198 ENSRNOP00000014377 1.2020864960788595 +ENSRNOP00000016871 ENSCINP00000010262 0.7998840304515645 ENSGALP00000060372 ENSRNOP00000014377 0.9656107168863438 ENSRNOP00000016871 ENSGALP00000028084 1.0358908406122709 ENSRNOP00000014377 ENSMODP00000006811 1.014568295990869 ENSRNOP00000016871 ENSMODP00000002384 0.9858168713252738 ENSCINP00000024362 ENSCAFP00000017344 0.5392752828930565 -ENSDARP00000154605 ENSCINP00000005198 1.491300131871246 -ENSCINP00000010262 ENSDARP00000149121 0.8499085703153215 +ENSCINP00000005198 ENSDARP00000154605 1.491300131871246 +ENSDARP00000149121 ENSCINP00000010262 0.8499085703153215 ENSCINP00000024362 ENSP00000260197 0.4937093636879676 -ENSGALP00000060372 ENSCINP00000005198 1.388829513749228 +ENSCINP00000005198 ENSGALP00000060372 1.388829513749228 ENSCINP00000010262 ENSGALP00000028084 1.0053941211274267 ENSCINP00000024362 ENSGALP00000046461 0.6139352479277681 -ENSMODP00000006811 ENSCINP00000005198 1.512341563219763 -ENSCINP00000010262 ENSMODP00000002384 1.01157228347777 +ENSCINP00000005198 ENSMODP00000006811 1.512341563219763 +ENSMODP00000002384 ENSCINP00000010262 1.01157228347777 ENSCINP00000024362 ENSMODP00000016287 0.4844878180487609 ENSGALP00000060372 ENSMUSP00000032440 0.9226253791108336 ENSGALP00000060372 ENSDARP00000147265 0.9787006097925798 ENSDARP00000154605 ENSGALP00000060372 0.9787006097925798 -ENSGALP00000028084 ENSDARP00000149121 0.8508452087136668 -ENSGALP00000060372 WBGene00003806.1 0.8967195494012699 +ENSDARP00000149121 ENSGALP00000028084 0.8508452087136668 +WBGene00003806.1 ENSGALP00000060372 0.8967195494012699 ENSGALP00000060372 ENSMODP00000006811 0.9202902491145213 ENSMODP00000002384 ENSGALP00000028084 0.966092055738595 -ENSGALP00000046461 ENSMODP00000016287 1.115319260624795 +ENSMODP00000016287 ENSGALP00000046461 1.115319260624795 ENSDARP00000154605 ENSMODP00000006811 1.115264423964748 -ENSMODP00000002384 ENSDARP00000149121 0.891019663837538 +ENSDARP00000149121 ENSMODP00000002384 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 c4e5425..5ac97e4 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 +ENSCAFP00000053904 ENSMUSP00000032440 ENSTNIP00000005325 ENSPTRP00000071151 ENSDARP00000071531 ENSDARP00000147265 ENSDARP00000154605 ENSP00000373312 WBGene00003806.1 ENSRNOP00000014377 ENSCINP00000005198 ENSMODP00000006811 ENSGALP00000060372 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 +ENSCAFP00000017344 ENSMUSP00000058613 ENSTNIP00000017394 ENSPTRP00000007532 ENSDARP00000129655 ENSP00000260197 ENSCINP00000024362 ENSGALP00000046461 ENSMODP00000016287 +ENSMUSP00000086314 ENSMUSP00000086311 ENSRNOP00000065522