diff --git a/dogma.py b/dogma.py
index 4a6b003aab37bb9fbdc539fdb1c788bf6cbe53d8..de31f39e6c59c970a12830de106b114f71560ff2 100755
--- a/dogma.py
+++ b/dogma.py
@@ -24,13 +24,13 @@
# for detailed information about the available command line arguments, use: python dogma.py --help or read the Manual
-
+from __future__ import print_function
import cPickle as Pickle
import re
from os.path import splitext, basename, isfile, dirname, realpath, isdir, abspath
from os.path import join as ospjoin
from os import listdir, makedirs, extsep
-from sys import argv
+import sys
from subprocess import call
from collections import defaultdict
from itertools import groupby, combinations
@@ -40,7 +40,6 @@ from argparse import RawTextHelpFormatter as HelpFormat
from hashlib import md5
import warnings
import gzip
-
# no external python libraries are required.
annotype = 'rad'
@@ -48,165 +47,168 @@ conversion_dictionary = None
def main():
- # top level argument parsing
- parser = ArgumentParser(prog='DOGMA', formatter_class=HelpFormat,
- description='DOGMA is a software that can assess transcriptome or proteome quality based on'
- ' conserved protein domains.\nTo score the domain completeness of a '
- 'proteome/transcriptome, DOGMA searches its domain annotation for conserved '
- 'domain arrangements (CDAs).\nBy default, the CDAs comprise domains that '
- 'are shared by six eukaryotic model species.\n\n'
- 'For more details please use one of the following commands:\n'
- 'python dogma.py proteome --help\n'
- 'python dogma.py transcriptome --help\n')
- subparsers = parser.add_subparsers(help='Program mode DOGMA should run (proteome or transcriptome analysis mode)',
- dest='mode')
- parser.add_argument("-v", "--version", action="version", version="DOGMA version 3.0")
-
- # proteome mode argument parsing
- parser_proteome = subparsers.add_parser("proteome", help="Analyse proteome data.")
- parser_proteome.add_argument("-a", "--annotation_file", action="store", type=str, default=None,
- help="Annotation file of the proteome to be quality checked as RADIANT or PfamScan output"
- " without short isoforms.")
- parser_proteome.add_argument("-i", "--initial_radiant_run", action="store", type=str, default=None,
- help="The proteome file (in fasta format) that should be used for an initial run "
- "of RADIANT (domain annotation) and subsequently analyzed with DOGMA. "
- "Just longest isoforms should be included in the fasta-file.")
- parser_proteome.add_argument("-r", "--reference_proteomes", action="store", type=str, default=None,
- help="A directory that contains annotation files of selected core species "
- "(*.rad for RADIANT annotated files and *.pfsc for PfamScan annotated files). "
- "Used to construct the core set with conserved domain arrangements. "
- "If omitted, the script looks for default values stored in the "
- "\"reference-sets/eukaryotes\" directory. Valid values for analysis with the "
- "default core sets are \"eukaryotes\", \"mammals\", \"insects\", \"bacteria\" and \"archaea\" "
- "(without quotes)")
- parser_proteome.add_argument("-c", "--CDA_count_cutoff", action="store", default=2, type=int,
- help="When determining the count of a specific CDA, this cutoff determines the "
- "maximum permitted difference in counts among the core species to include "
- "the specific CDA to the core set (default=2).")
- parser_proteome.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, B-C-D).")
- 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="31",
- help="The version number of the pfam database that should be used (Default is 31).")
- 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)")
-
- # transcriptome mode argument parsing
- parser_transcriptome = subparsers.add_parser("transcriptome", help="Analyse transcriptome data.")
- parser_transcriptome.add_argument("-a", "--annotation_file", action="store", type=str, default=None,
- help="Annotation file of the transcriptome to be quality checked as"
- "RADIANT or PfamScan output.")
- parser_transcriptome.add_argument("-i", "--initial_radiant_run", action="store", type=str, default=None,
- help="The transcriptome file (in fasta format) that should be used for an initial"
- " run of RADIANT (domain annotation) and subsequently analyzed with DOGMA.")
- parser_transcriptome.add_argument("-r", "--reference_transcriptomes", action="store", type=str, default=None,
- help="A directory that contains annotation files of selected core species "
- "(*.rad for RADIANT annotated files and *.pfsc for pfam scan annotated "
- "files). Used to construct the core set with conserved domain arrangements. "
- "If omitted, the script looks for default values stored in the "
- "\"pfamXX/reference-sets/eukaryotes\" directory. Valid values for analysis with the"
- " default core sets are \"eukaryotes\", \"mammals\", \"insects\", \"bacteria\" and \"archaea\" "
- "(without quotes)")
- parser_transcriptome.add_argument("-o", "--outfile", action="store", default=None,
- help="Summary will be saved in a file with the given name (and path), "
- "instead of printed in the console.")
- 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="31",
- help="The version number of the pfam database that should be used "
- "(Default is 31).")
- 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)")
-
- args = parser.parse_args()
-
- global annotype
- global conversion_dictionary
- conversion_dictionary = ConversionDictionary(args.pfam)
-
- if args.mode == 'proteome':
- if args.initial_radiant_run is not None:
- try:
- # initial run of RADIANT with a proteome
- radiant_path = abspath(find_executable('radiant'))[:-7]
- if args.database is None:
- database = radiant_path[:-6] + 'pfam' + args.pfam
- else:
- database = args.database
- 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.")
-
- if args.annotation_file is None:
- parser.error('No input file specified. Please use -a or -i option to specify the proteome input file.')
-
- if args.annotation_file is not None:
- with open(args.annotation_file, 'rb') as fi:
- firstline = fi.readline()
- if re.search('pfam_scan.pl', firstline):
- annotype = 'pfsc'
- elif re.search('RADIANT', firstline):
- annotype = 'rad'
- else:
- raise IOError('Type of annotation file could not be detected. Please make sure input is a standard PfamScan or RADIANT annotation.')
-
- if args.reference_proteomes is None:
- args.reference_proteomes = 'eukaryotes'
-
- print ('# running python dogma.py v3.0 proteome -a {} -r {} -c {} -s {} -o {} -m {}'.format(
- args.annotation_file, args.reference_proteomes, args.CDA_count_cutoff,
- args.cda_size, args.outfile, args.pfam))
-
- # starting the main method with the specified parameters
- score_single_proteome(args.annotation_file, args.outfile, args.CDA_count_cutoff,
- args.cda_size, args.reference_proteomes, args.mode, args.pfam)
-
- elif args.mode == 'transcriptome':
- if args.initial_radiant_run is not None:
- try:
- # initial run of RADIANT with a transcriptome
- radiant_path = abspath(find_executable('radiant'))[:-7]
- if args.database is None:
- database = radiant_path[:-6] + 'pfam' + args.pfam
- else:
- database = args.database
- call(['radiant', '-i', args.initial_radiant_run, '--translate', '-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.")
-
- if args.annotation_file is None:
- parser.error(
- 'No input file specified. Please use -a or -i option to specify the transcriptome input '
- 'file.')
-
- if args.annotation_file is not None:
- with open(args.annotation_file, 'rb') as fi:
- firstline = fi.readline()
- if re.search('pfam_scan.pl', firstline):
- annotype = 'pfsc'
- elif re.search('RADIANT', firstline):
- annotype = 'rad'
- else:
- raise IOError(
- 'Type of annotation file could not be detected. Please make sure input is a standard PfamScan or RADIANT annotation.')
-
- if args.reference_transcriptomes is None:
- args.reference_transcriptomes = 'eukaryotes'
- print ('# running python dogma.py v3.0 transcriptome -i {} -s {} -a {} -r {} -o {} -m {}'.format(
- args.initial_radiant_run, args.cda_size, args.annotation_file,
- args.reference_transcriptomes, args.outfile, args.pfam))
- score_single_transcriptome(args.annotation_file, args.outfile, args.cda_size, args.reference_transcriptomes,
- args.mode, args.pfam)
+ try:
+ # top level argument parsing
+ parser = ArgumentParser(prog='DOGMA', formatter_class=HelpFormat,
+ description='DOGMA is a software that can assess transcriptome or proteome quality based on'
+ ' conserved protein domains.\nTo score the domain completeness of a '
+ 'proteome/transcriptome, DOGMA searches its domain annotation for conserved '
+ 'domain arrangements (CDAs).\nBy default, the CDAs comprise domains that '
+ 'are shared by six eukaryotic model species.\n\n'
+ 'For more details please use one of the following commands:\n'
+ 'python dogma.py proteome --help\n'
+ 'python dogma.py transcriptome --help\n')
+ subparsers = parser.add_subparsers(help='Program mode DOGMA should run (proteome or transcriptome analysis mode)',
+ dest='mode')
+ parser.add_argument("-v", "--version", action="version", version="DOGMA version 3.0")
+
+ # proteome mode argument parsing
+ parser_proteome = subparsers.add_parser("proteome", help="Analyse proteome data.")
+ parser_proteome.add_argument("-a", "--annotation_file", action="store", type=str, default=None,
+ help="Annotation file of the proteome to be quality checked as RADIANT or PfamScan output"
+ " without short isoforms.")
+ parser_proteome.add_argument("-i", "--initial_radiant_run", action="store", type=str, default=None,
+ help="The proteome file (in fasta format) that should be used for an initial run "
+ "of RADIANT (domain annotation) and subsequently analyzed with DOGMA. "
+ "Just longest isoforms should be included in the fasta-file.")
+ parser_proteome.add_argument("-r", "--reference_proteomes", action="store", type=str, default=None,
+ help="A directory that contains annotation files of selected core species "
+ "(*.rad for RADIANT annotated files and *.pfsc for PfamScan annotated files). "
+ "Used to construct the core set with conserved domain arrangements. "
+ "If omitted, the script looks for default values stored in the "
+ "\"reference-sets/eukaryotes\" directory. Valid values for analysis with the "
+ "default core sets are \"eukaryotes\", \"mammals\", \"insects\", \"bacteria\" and \"archaea\" "
+ "(without quotes)")
+ parser_proteome.add_argument("-c", "--CDA_count_cutoff", action="store", default=2, type=int,
+ help="When determining the count of a specific CDA, this cutoff determines the "
+ "maximum permitted difference in counts among the core species to include "
+ "the specific CDA to the core set (default=2).")
+ parser_proteome.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, B-C-D).")
+ 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="31",
+ help="The version number of the pfam database that should be used (Default is 31).")
+ 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)")
+
+ # transcriptome mode argument parsing
+ parser_transcriptome = subparsers.add_parser("transcriptome", help="Analyse transcriptome data.")
+ parser_transcriptome.add_argument("-a", "--annotation_file", action="store", type=str, default=None,
+ help="Annotation file of the transcriptome to be quality checked as"
+ "RADIANT or PfamScan output.")
+ parser_transcriptome.add_argument("-i", "--initial_radiant_run", action="store", type=str, default=None,
+ help="The transcriptome file (in fasta format) that should be used for an initial"
+ " run of RADIANT (domain annotation) and subsequently analyzed with DOGMA.")
+ parser_transcriptome.add_argument("-r", "--reference_transcriptomes", action="store", type=str, default=None,
+ help="A directory that contains annotation files of selected core species "
+ "(*.rad for RADIANT annotated files and *.pfsc for pfam scan annotated "
+ "files). Used to construct the core set with conserved domain arrangements. "
+ "If omitted, the script looks for default values stored in the "
+ "\"pfamXX/reference-sets/eukaryotes\" directory. Valid values for analysis with the"
+ " default core sets are \"eukaryotes\", \"mammals\", \"insects\", \"bacteria\" and \"archaea\" "
+ "(without quotes)")
+ parser_transcriptome.add_argument("-o", "--outfile", action="store", default=None,
+ help="Summary will be saved in a file with the given name (and path), "
+ "instead of printed in the console.")
+ 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="31",
+ help="The version number of the pfam database that should be used "
+ "(Default is 31).")
+ 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)")
+
+ args = parser.parse_args()
+ global annotype
+ global conversion_dictionary
+ conversion_dictionary = ConversionDictionary(args.pfam)
+
+ if args.mode == 'proteome':
+ if args.initial_radiant_run is not None:
+ try:
+ # initial run of RADIANT with a proteome
+ radiant_path = abspath(find_executable('radiant'))[:-7]
+ if args.database is None:
+ database = radiant_path[:-6] + 'pfam' + args.pfam
+ else:
+ database = args.database
+ 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.")
+
+ if args.annotation_file is None:
+ parser.error('No input file specified. Please use -a or -i option to specify the proteome input file.')
+
+ if args.annotation_file is not None:
+ with open(args.annotation_file, 'rb') as fi:
+ firstline = fi.readline()
+ if re.search('pfam_scan.pl', firstline):
+ annotype = 'pfsc'
+ elif re.search('RADIANT', firstline):
+ annotype = 'rad'
+ else:
+ raise IOError('Type of annotation file could not be detected. Please make sure input is a standard PfamScan or RADIANT annotation.')
+
+ if args.reference_proteomes is None:
+ args.reference_proteomes = 'eukaryotes'
+
+ print ('# running python dogma.py v3.0 proteome -a {} -r {} -c {} -s {} -o {} -m {}'.format(
+ args.annotation_file, args.reference_proteomes, args.CDA_count_cutoff,
+ args.cda_size, args.outfile, args.pfam))
+
+ # starting the main method with the specified parameters
+ score_single_proteome(args.annotation_file, args.outfile, args.CDA_count_cutoff,
+ args.cda_size, args.reference_proteomes, args.mode, args.pfam)
+
+ elif args.mode == 'transcriptome':
+ if args.initial_radiant_run is not None:
+ try:
+ # initial run of RADIANT with a transcriptome
+ radiant_path = abspath(find_executable('radiant'))[:-7]
+ if args.database is None:
+ database = radiant_path[:-6] + 'pfam' + args.pfam
+ else:
+ database = args.database
+ call(['radiant', '-i', args.initial_radiant_run, '--translate', '-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.")
+
+ if args.annotation_file is None:
+ parser.error(
+ 'No input file specified. Please use -a or -i option to specify the transcriptome input '
+ 'file.')
+
+ if args.annotation_file is not None:
+ with open(args.annotation_file, 'rb') as fi:
+ firstline = fi.readline()
+ if re.search('pfam_scan.pl', firstline):
+ annotype = 'pfsc'
+ elif re.search('RADIANT', firstline):
+ annotype = 'rad'
+ else:
+ raise IOError(
+ 'Type of annotation file could not be detected. Please make sure input is a standard PfamScan or RADIANT annotation.')
+
+ if args.reference_transcriptomes is None:
+ args.reference_transcriptomes = 'eukaryotes'
+ print ('# running python dogma.py v3.0 transcriptome -i {} -s {} -a {} -r {} -o {} -m {}'.format(
+ args.initial_radiant_run, args.cda_size, args.annotation_file,
+ args.reference_transcriptomes, args.outfile, args.pfam))
+ score_single_transcriptome(args.annotation_file, args.outfile, args.cda_size, args.reference_transcriptomes,
+ args.mode, args.pfam)
+ except Exception, e:
+ print("Error! " + str(e), file=sys.stderr)
+ sys.exit(1)
class ConversionDictionary(dict):
"""
@@ -221,7 +223,7 @@ class ConversionDictionary(dict):
self['acc_to_dom'] = defaultdict(str)
self['dom_to_type'] = defaultdict(str)
- script_path = dirname(realpath(argv[0])) # the path where the script dogma.py is located.
+ script_path = dirname(realpath(sys.argv[0])) # the path where the script dogma.py is located.
pfama = script_path + '/pfam' + str(pfam_version) + '/pfamA.txt'
if pfam_version == 28:
@@ -257,7 +259,7 @@ def score_single_transcriptome(annotation_file, outfile=None, max_dom_tup_len=3,
global annotype
- script_path = dirname(realpath(argv[0]))
+ script_path = dirname(realpath(sys.argv[0]))
at = annotype
if hq_transcriptomes in ('eukaryotes', 'mammals', 'insects', 'bacteria', 'archaea'):
@@ -333,7 +335,7 @@ def score_single_proteome(annotation_file, outfile=None, cutoff=2,
global annotype
- script_path = dirname(realpath(argv[0]))
+ script_path = dirname(realpath(sys.argv[0]))
at = annotype
if hq_proteomes in ('eukaryotes', 'mammals', 'insects', 'bacteria', 'archaea'):
@@ -566,7 +568,7 @@ class SpeciesComparer(dict):
self.domain_file_paths_iterable = domain_file_paths_iterable
self.max_count_difference_in_HQ_cutoff = cutoff
self.dom_tuple_len = dom_tuple_len
- self.script_path = dirname(realpath(argv[0]))
+ self.script_path = dirname(realpath(sys.argv[0]))
self.mode = mode
self.pfam = pfam
self.default_path = (ospjoin(self.script_path, 'reference-sets', 'eukaryotes'),