diff --git a/dogma.py b/dogma.py index 4a6b003aab37bb9fbdc539fdb1c788bf6cbe53d8..3ee47f55a8d94c3e4d899bd3cb024467f45c19c7 100755 --- a/dogma.py +++ b/dogma.py @@ -67,7 +67,7 @@ def main(): 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, + parser_proteome.add_argument("-i", "--initial_radiant_run", action="store", type=str, default=None, metavar='SEQUENCE_FILE', 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.") @@ -100,7 +100,7 @@ def main(): 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, + parser_transcriptome.add_argument("-i", "--initial_radiant_run", action="store", type=str, default=None, metavar='SEQUENCE_FILE', 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, @@ -786,12 +786,13 @@ class Summary: Prints a human-readable summary of the domain completeness report. """ str1 = "\n".join( - ["\nStatistics of the completeness of the {} ", + ["\nRunning python dogma.py v{} {} -i {} -s {} -a {} -r {} -o {} -m {}\n", + "Statistics of the completeness of the {} ", "- {} -", "based on {} single-domain CDAs and {} multiple-domain CDAs\n " "({} was used as core set for this analysis):\n", "CDAsize\t#Found\t#Expct\t%Completeness\n"] - ).format(self.mode, self.species_name, self.num_single_cdas, self.num_cda_tuples, self.corespecies) + ).format(self.version, self.mode, self.initial, self.s, self.annotation_file, self.corespecies, ,self.mode, self.species_name, self.num_single_cdas, self.num_cda_tuples, self.corespecies) str2_list = [] str4_list = []