Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.py @ 9:43341e97bb08 draft

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Uploaded
author greg
date Mon, 10 Apr 2017 12:47:18 -0400
parents 529f4635ddb4
children af8dad310c32
comparison
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8:9e68bebb3d7c 9:43341e97bb08
11 parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method') 11 parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method')
12 parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help="Trims alignments using trimAl's ML heuristic trimming approach") 12 parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help="Trims alignments using trimAl's ML heuristic trimming approach")
13 parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments") 13 parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments")
14 parser.add_argument('--gap_trimming', dest='gap_trimming', default=None, type=float, help='Remove sites in alignments with gaps of') 14 parser.add_argument('--gap_trimming', dest='gap_trimming', default=None, type=float, help='Remove sites in alignments with gaps of')
15 parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=None, help='"Maximum number of iterations') 15 parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=None, help='"Maximum number of iterations')
16 parser.add_argument('--method', dest='method', help='Protein clustering method')
17 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') 16 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
18 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets") 17 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help="Directory of input fasta datasets")
19 parser.add_argument('--output', dest='output', help="Output dataset") 18 parser.add_argument('--output', dest='output', help="Output dataset")
20 parser.add_argument('--output_dir', dest='output_dir', help="Output dataset file_path directory") 19 parser.add_argument('--output_dir', dest='output_dir', help="Output dataset files_path directory")
21 parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='"Maximum number of iteration that the PASTA algorithm will execute') 20 parser.add_argument('--pasta_iter_limit', dest='pasta_iter_limit', type=int, default=None, help='"Maximum number of iteration that the PASTA algorithm will execute')
22 parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta') 21 parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
23 parser.add_argument('--remove_sequences', dest='remove_sequences', default=None, type=float, help='Remove sequences with gaps of') 22 parser.add_argument('--remove_sequences', dest='remove_sequences', default=None, type=float, help='Remove sequences with gaps of')
24 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold')
25 23
26 args = parser.parse_args() 24 args = parser.parse_args()
27 25
28 # Build the command line. 26 # Build the command line.
29 cmd = 'GeneFamilyAligner' 27 cmd = 'GeneFamilyAligner'
30 cmd += ' --orthogroup_faa %s' % args.orthogroup_faa 28 cmd += ' --orthogroup_faa %s' % args.orthogroup_faa
31 cmd += ' --scaffold %s' % args.scaffold
32 cmd += ' --method %s' % args.method
33 cmd += ' --alignment_method %s' % args.alignment_method 29 cmd += ' --alignment_method %s' % args.alignment_method
34 if args.alignment_method == 'pasta': 30 if args.alignment_method == 'pasta':
35 if args.pasta_script_path is not None: 31 if args.pasta_script_path is not None:
36 cmd += ' --pasta_script_path %s' % args.pasta_script_path 32 cmd += ' --pasta_script_path %s' % args.pasta_script_path
37 if args.pasta_iter_limit is not None: 33 if args.pasta_iter_limit is not None: