Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.py @ 25:93b1207562d3 draft

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author greg
date Fri, 05 May 2017 09:31:30 -0400
parents af8dad310c32
children 71ba5e9cf1dd
comparison
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24:6d34db10765c 25:93b1207562d3
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import argparse 2 import argparse
3 import os 3 import os
4 import subprocess
5 4
6 import utils 5 import utils
7 6
8 OUTPUT_DIR = 'geneFamilyAlignments_dir' 7 OUTPUT_DIR = 'geneFamilyAlignments_dir'
9 8
10 parser = argparse.ArgumentParser() 9 parser = argparse.ArgumentParser()
11 parser.add_argument('--alignment_method', dest='alignment_method', help='Multiple sequence alignments method') 10 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") 11 parser.add_argument('--automated_trimming', dest='automated_trimming', default=None, help='Trims alignments using trimAls ML heuristic trimming approach')
13 parser.add_argument('--codon_alignments', dest='codon_alignments', default=None, help="Flag for constructing orthogroup multiple codon alignments") 12 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=0, type=float, help='Remove sites in alignments with gaps of') 13 parser.add_argument('--gap_trimming', dest='gap_trimming', default=0, type=float, help='Remove sites in alignments with gaps of')
15 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')
16 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')
17 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')
18 parser.add_argument('--output', dest='output', help="Output dataset") 17 parser.add_argument('--output', dest='output', help='Output dataset')
19 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')
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') 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')
21 parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta') 20 parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
22 parser.add_argument('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of') 21 parser.add_argument('--remove_sequences', dest='remove_sequences', default=0, type=float, help='Remove sequences with gaps of')
23 22
24 args = parser.parse_args() 23 args = parser.parse_args()
25 24
41 cmd += ' --gap_trimming %4f' % args.gap_trimming 40 cmd += ' --gap_trimming %4f' % args.gap_trimming
42 if args.remove_sequences > 0: 41 if args.remove_sequences > 0:
43 cmd += ' --remove_sequences %4f' % args.remove_sequences 42 cmd += ' --remove_sequences %4f' % args.remove_sequences
44 if args.iterative_realignment > 0: 43 if args.iterative_realignment > 0:
45 cmd += ' --iterative_realignment %d' % args.iterative_realignment 44 cmd += ' --iterative_realignment %d' % args.iterative_realignment
45
46 # Run the command. 46 # Run the command.
47 proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) 47 utils.run_command(cmd)
48 rc = proc.wait() 48
49 utils.check_execution_errors(rc, proc.stderr) 49 # Handle outputs.
50 if args.codon_alignments is None: 50 if args.codon_alignments is None:
51 src_output_dir = OUTPUT_DIR 51 src_output_dir = OUTPUT_DIR
52 else: 52 else:
53 src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln') 53 src_output_dir = os.path.join(OUTPUT_DIR, 'orthogroups_aln')
54 utils.move_directory_files(src_output_dir, args.output_dir) 54 utils.move_directory_files(src_output_dir, args.output_dir)