diff --git a/CHANGELOG b/CHANGELOG
index 36794ba6de53340b46cf27078b63befa463e221f..95b267a552857192a7cde0cd7d684ccd8010beb6 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,5 +1,11 @@
+DOGMA 3.8
+=========
+
+- update to Pfam Database version 36 (default for DOGMA from this version on)
+
DOGMA 3.7
=========
+
- update to Pfam Database version 35 (default for DOGMA from this version on)
- runs with new RADIANT version 1.0
- updated error handling for initial RADIANT annotation of fasta files if RADIANT is not in the PATH variable
diff --git a/README.md b/README.md
index 4a861b650024133b7a0b2dc89f9d4e271f5afd9f..dea6389e5d77988594ab8f0335e6bf568cb2bd31 100644
--- a/README.md
+++ b/README.md
@@ -16,7 +16,7 @@ Current dependencies are (but you will need just one of them):
- RADIANT (https://domainworld.uni-muenster.de/programs/radiant/)
OR
-- pfam_scan.pl (ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/)
+- pfam_scan.pl (http://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/)
Furthermore you will need a core set to run DOGMA.
diff --git a/UserManual.pdf b/UserManual.pdf
old mode 100644
new mode 100755
index 34b82ae26159fcf201d9ce9989769aefb153bf23..20f664d16e4aff7fd5307f235a641f50997a77d5
Binary files a/UserManual.pdf and b/UserManual.pdf differ
diff --git a/dogma.py b/dogma.py
index d34fcd41aff9bd58b08e822d3598f08c287d802f..c7faf97c5ae96759064db5f2438291f4c83d1dbe 100755
--- a/dogma.py
+++ b/dogma.py
@@ -1,13 +1,13 @@
#!/usr/bin/env python
-# DOGMA version 3.7
+# DOGMA version 3.8
# DOGMA is a python script that can assess proteome or transcriptome quality based on conserved protein domains.
# To score the domain completeness of a proteome or transcriptome, DOGMA searches its domain annotation for conserved
# domains. By default, the conserved domains comprise domains that are shared by six eukaryotic model species.
# Copyright (C) 2015-2023 Elias Dohmen
-# <e.dohmen@wwu.de> based on code by Lukas Kremer.
+# <e.dohmen@uni-muenster.de> based on code by Lukas Kremer.
# DOGMA is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
@@ -48,7 +48,7 @@ conversion_dictionary = None
def main():
- dogma_version = '3.7'
+ dogma_version = '3.8'
try:
# top level argument parsing
@@ -94,8 +94,8 @@ def main():
parser_proteome.add_argument("-o", "--outfile", action="store", type=str, default=None,
help="Summary will be saved in a file with the given name (and path), "
"instead of printed in the console.")
- parser_proteome.add_argument("-m", "--pfam", action="store", type=str, default="35",
- help="The version number of the pfam database that should be used (Default is 35).")
+ parser_proteome.add_argument("-m", "--pfam", action="store", type=str, default="36",
+ help="The version number of the pfam database that should be used (Default is 36).")
parser_proteome.add_argument("-d", "--database", action="store", type=str, default=None,
help="If the RADIANT database is not located in the RADIANT directory, please specify"
" path and name of the database. (Just necessary for -i option)")
@@ -126,9 +126,9 @@ def main():
parser_transcriptome.add_argument("-s", "--cda_size", action="store", default=3, type=int,
help="Specifies up to which size subsets of CDAs should be considered "
"(default=3; A-B-C-D --> A-B-C, A-B-D, B-C-D etc.).")
- parser_transcriptome.add_argument("-m", "--pfam", action="store", type=str, default="35",
+ parser_transcriptome.add_argument("-m", "--pfam", action="store", type=str, default="36",
help="The version number of the pfam database that should be used "
- "(Default is 35).")
+ "(Default is 36).")
parser_transcriptome.add_argument("-d", "--database", action="store", default=None,
help="If the RADIANT database is not located in the RADIANT directory, please specify"
" path and name of the database. (Just necessary for -i option)")
@@ -267,7 +267,7 @@ class ConversionDictionary(dict):
def score_single_transcriptome(annotation_file, outfile=None, max_dom_tup_len=3,
- hq_transcriptomes=None, mode='transcriptome', pfam='35', initial=None, version='3.7',
+ hq_transcriptomes=None, mode='transcriptome', pfam='36', initial=None, version='3.8',
annotype='pfsc', coverage=0.5):
"""
combines the functions and classes to score a sample proteome in terms of it's domain completeness.
@@ -345,7 +345,7 @@ def score_single_transcriptome(annotation_file, outfile=None, max_dom_tup_len=3,
def score_single_proteome(annotation_file, outfile=None, cutoff=2,
- max_dom_tup_len=3, hq_proteomes=None, mode='proteome', pfam='35', initial=None, version='3.7',
+ max_dom_tup_len=3, hq_proteomes=None, mode='proteome', pfam='36', initial=None, version='3.8',
annotype='pfsc', coverage=0.5):
"""
combines the functions and classes to score a sample proteome in terms of it's domain completeness.
@@ -776,7 +776,7 @@ class QualityChecker:
if count_in_candidate < count_in_HQ:
self.doms_missing_number += count_in_HQ - count_in_candidate
self.out.append((count_in_candidate, self.cda_count_dict[dom], dom))
- self.out.sort(key=lambda l: l[2])
+ self.out.sort(key=lambda ele: ele[2])
if self.number_of_CDA == 0:
self.percentage = "NA"