Mercurial > repos > greg > plant_tribes_gene_family_aligner

comparison gene_family_aligner.py @ 1:ab1f0bab96f3 draft

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author greg
date Tue, 01 Aug 2017 14:25:14 -0400
parents 7ba9469800b9
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0:7ba9469800b9 1:ab1f0bab96f3
14 parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=0, help='Maximum number of iterations') 14 parser.add_argument('--iterative_realignment', dest='iterative_realignment', type=int, default=0, help='Maximum number of iterations')
15 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') 15 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution')
16 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets') 16 parser.add_argument('--orthogroup_faa', dest='orthogroup_faa', help='Directory of input fasta datasets')
17 parser.add_argument('--output', dest='output', help='Output dataset') 17 parser.add_argument('--output', dest='output', help='Output dataset')
18 parser.add_argument('--output_dir', dest='output_dir', help='Output dataset files_path directory') 18 parser.add_argument('--output_dir', dest='output_dir', help='Output dataset files_path directory')
19 parser.add_argument('--output_dataset_collection', dest='output_dataset_collection', default=None, help='Output additional dataset collection of files.')
19 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')
20 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')
21 parser.add_argument('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of') 22 parser.add_argument('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of')
22 23
23 args = parser.parse_args() 24 args = parser.parse_args()
49 # Handle outputs. 50 # Handle outputs.
50 if args.codon_alignments is None: 51 if args.codon_alignments is None:
51 src_output_dir = OUTPUT_DIR 52 src_output_dir = OUTPUT_DIR
52 else: 53 else:
53 src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln') 54 src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln')
55 if args.output_dataset_collection is not None:
56 utils.move_directory_files(src_output_dir, args.output_dataset_collection, copy=True)
54 utils.move_directory_files(src_output_dir, args.output_dir) 57 utils.move_directory_files(src_output_dir, args.output_dir)
55 utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir) 58 utils.write_html_output(args.output, 'Aligned gene family sequences', args.output_dir)