diff --git a/CHANGELOG b/CHANGELOG
index 4fb7395b09ecef845a62a860f0856803aac52020..36794ba6de53340b46cf27078b63befa463e221f 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,9 @@
+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
+
DOGMA 3.6
=========
diff --git a/README.md b/README.md
index 71b47bce9fcd62c5c6015ca01311443fba12e707..4a861b650024133b7a0b2dc89f9d4e271f5afd9f 100644
--- a/README.md
+++ b/README.md
@@ -12,7 +12,7 @@ Requirements
------------
We try to keep the dependencies as little as possible.
-Current dependencies are (but you will just need one of them):
+Current dependencies are (but you will need just one of them):
- RADIANT (https://domainworld.uni-muenster.de/programs/radiant/)
OR
diff --git a/UserManual.pdf b/UserManual.pdf
index f2bd809240f99d7dee6c9baa1acbf8540bbaed24..34b82ae26159fcf201d9ce9989769aefb153bf23 100644
Binary files a/UserManual.pdf and b/UserManual.pdf differ
diff --git a/dogma.py b/dogma.py
index fa01976b61feacea7f190c92f6a6bc4d3f4a7693..d34fcd41aff9bd58b08e822d3598f08c287d802f 100755
--- a/dogma.py
+++ b/dogma.py
@@ -1,12 +1,12 @@
#!/usr/bin/env python
-# DOGMA version 3.6
+# DOGMA version 3.7
# 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) 2015-2021 Elias Dohmen
+# Copyright (C) 2015-2023 Elias Dohmen
# <e.dohmen@wwu.de> based on code by Lukas Kremer.
# DOGMA is free software: you can redistribute it and/or modify it
@@ -48,7 +48,7 @@ conversion_dictionary = None
def main():
- dogma_version = '3.6'
+ dogma_version = '3.7'
try:
# top level argument parsing
@@ -94,15 +94,14 @@ 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="34",
- help="The version number of the pfam database that should be used (Default is 34).")
+ 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("-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)")
parser_proteome.add_argument("-cov", "--coverage", action="store", default=0.5, type=float,
help="Specifies how much of a domain has to be annotated to count as a partial domain. Default=0.5 "
- "This would mean if less than 50%% of the domain is annotated, it is considered a partial domain. "
- "The partial domain analysis is just available with PfamScan annotations.")
+ "This would mean if less than 50%% of the domain is annotated, it is considered a partial domain.")
# transcriptome mode argument parsing
parser_transcriptome = subparsers.add_parser("transcriptome", help="Analyse transcriptome data.")
@@ -127,16 +126,15 @@ 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="34",
+ parser_transcriptome.add_argument("-m", "--pfam", action="store", type=str, default="35",
help="The version number of the pfam database that should be used "
- "(Default is 34).")
+ "(Default is 35).")
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)")
parser_transcriptome.add_argument("-cov", "--coverage", action="store", default=0.5, type=float,
help="Specifies how much of a domain has to be annotated to count as a partial domain. Default=0.5 "
- "This would mean if less than 50%% of the domain is annotated, it is considered a partial domain. "
- "The partial domain analysis is just available with PfamScan annotations.")
+ "This would mean if less than 50%% of the domain is annotated, it is considered a partial domain.")
args = parser.parse_args()
@@ -159,8 +157,8 @@ def main():
call(['radiant', '-i', args.initial_radiant_run, '-d', database, '-o',
args.initial_radiant_run + '.rad'])
args.annotation_file = args.initial_radiant_run + '.rad'
- except AttributeError:
- raise AttributeError("No valid installation of RADIANT found.")
+ except TypeError:
+ raise RuntimeError("No valid installation of RADIANT found.")
if args.annotation_file is None:
parser.error('No input file specified. Please use -a or -i option to specify the proteome input file.')
@@ -269,7 +267,7 @@ class ConversionDictionary(dict):
def score_single_transcriptome(annotation_file, outfile=None, max_dom_tup_len=3,
- hq_transcriptomes=None, mode='transcriptome', pfam='34', initial=None, version='3.6',
+ hq_transcriptomes=None, mode='transcriptome', pfam='35', initial=None, version='3.7',
annotype='pfsc', coverage=0.5):
"""
combines the functions and classes to score a sample proteome in terms of it's domain completeness.
@@ -347,7 +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='34', initial=None, version='3.6',
+ max_dom_tup_len=3, hq_proteomes=None, mode='proteome', pfam='35', initial=None, version='3.7',
annotype='pfsc', coverage=0.5):
"""
combines the functions and classes to score a sample proteome in terms of it's domain completeness.
@@ -477,6 +475,7 @@ class DomainCounter(dict):
domain_start_pos = int(line[1])
domain_name = re.match('([^.]+)', line[3]).group(1)
arrangement_dict[seq_id].append((domain_start_pos, domain_name))
+
else:
raise NotImplementedError(
"File format couldn't be detected. Please make sure you use RADIANT or "
@@ -510,6 +509,7 @@ class DomainCounter(dict):
domain_start_pos = int(line[1])
domain_name = re.match('([^.]+)', line[3]).group(1)
arrangement_dict[seq_id].append((domain_start_pos, domain_name))
+
else:
raise NotImplementedError(
"File format couldn't be detected. Please make sure you use RADIANT or "