added support for different substitution matrices

JLSteenwyk · Aug 25, 2024 · ae122bc · ae122bc
1 parent ff65c7c
commit ae122bc
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Showing 125 changed files with 588 additions and 588 deletions.
diff --git 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
@@ -38,14 +38,14 @@ def write_user_args(
     print(
         textwrap.dedent(
             f"""\
-          ____       _   _           _    _ __  __ __  __ 
-         / __ \     | | | |         | |  | |  \/  |  \/  |
-        | |  | |_ __| |_| |__   ___ | |__| | \  / | \  / |
-        | |  | | '__| __| '_ \ / _ \|  __  | |\/| | |\/| |
-        | |__| | |  | |_| | | | (_) | |  | | |  | | |  | |
-         \____/|_|   \__|_| |_|\___/|_|  |_|_|  |_|_|  |_|
+      ____       _   _           _    _ __  __ __  __ 
+     / __ \     | | | |         | |  | |  \/  |  \/  |
+    | |  | |_ __| |_| |__   ___ | |__| | \  / | \  / |
+    | |  | | '__| __| '_ \ / _ \|  __  | |\/| | |\/| |
+    | |__| | |  | |_| | | | (_) | |  | | |  | | |  | |
+     \____/|_|   \__|_| |_|\___/|_|  |_|_|  |_|_|  |_|
 
-        Version: {__version__}
+    Version: {__version__}
 
     -------------
     | Arguments |

diff --git a/...is_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt b/...is_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt
@@ -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/...abditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt b/...abditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt
@@ -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/...enorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt b/...enorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt
@@ -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/.../Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt b/.../Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt
@@ -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/...aenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt b/...aenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt
@@ -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/...Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt b/...Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt
@@ -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/...tis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt b/...tis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt
@@ -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/...Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt b/...Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt
@@ -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/...bditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt b/...bditis_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/...abditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt b/...abditis_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/..._elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt b/..._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]