Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.py @ 2:01c08c35d051 draft

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Uploaded
author greg
date Fri, 07 Apr 2017 13:19:26 -0400
parents 6accbd3a1449
children 962feb5f0818
comparison
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1:4f1c3b8c9ab1 2:01c08c35d051
34 if args.pasta_script_path is not None: 34 if args.pasta_script_path is not None:
35 cmd += ' --pasta_script_path %s' % args.pasta_script_path 35 cmd += ' --pasta_script_path %s' % args.pasta_script_path
36 if args.pasta_iter_limit is not None: 36 if args.pasta_iter_limit is not None:
37 cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit 37 cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit
38 cmd += ' --num_threads %d' % args.num_threads 38 cmd += ' --num_threads %d' % args.num_threads
39 if args.orthogroup_fna is not None: 39 if args.codon_alignments is not None:
40 cmd += ' --orthogroup_fna' 40 cmd += ' --codon_alignments'
41 if args.automated_trimming is not None: 41 if args.automated_trimming is not None:
42 cmd += ' --automated_trimming' 42 cmd += ' --automated_trimming'
43 if args.gap_trimming is not None: 43 if args.gap_trimming is not None:
44 cmd += ' --gap_trimming %4f' % args.gap_trimming 44 cmd += ' --gap_trimming %4f' % args.gap_trimming
45 if args.remove_sequences is not None: 45 if args.remove_sequences is not None: