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comparison phylogenomics_analysis.py @ 68:5f76ffe55d0f draft

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author greg
date Tue, 28 Feb 2017 11:10:33 -0500
parents a0c347192b08
children 98c2a9f97e83
comparison
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67:43252277cb23 68:5f76ffe55d0f
19 parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help="Flag for coding sequences associated with orthogroups") 19 parser.add_argument('--orthogroup_fna', dest='orthogroup_fna', default=None, help="Flag for coding sequences associated with orthogroups")
20 parser.add_argument('--sequence_type', dest='sequence_type', default=None, help="Sequence type used in the phylogenetic inference") 20 parser.add_argument('--sequence_type', dest='sequence_type', default=None, help="Sequence type used in the phylogenetic inference")
21 parser.add_argument('--alignments_method', dest='alignments_method', default=None, help='Multiple sequence alignments method') 21 parser.add_argument('--alignments_method', dest='alignments_method', default=None, help='Multiple sequence alignments method')
22 parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta') 22 parser.add_argument('--pasta_script_path', dest='pasta_script_path', default=None, help='Path to script for executing pasta')
23 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') 23 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')
24 parser.add_argument('--tree_inference', dest='single_copy_custom', default=None, help='Phylogenetic trees inference method') 24 parser.add_argument('--tree_inference', dest='tree_inference', default=None, help='Phylogenetic trees inference method')
25 parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees') 25 parser.add_argument('--rooting_order', dest='rooting_order', default=None, help='Rooting order configuration for rooting trees')
26 parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis') 26 parser.add_argument('--bootstrap_replicates', dest='bootstrap_replicates', type=int, default=None, help='Number of replicates for rapid bootstrap analysis')
27 parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, default=None, help='Maximum number of sequences in orthogroup alignments') 27 parser.add_argument('--max_orthogroup_size', dest='max_orthogroup_size', type=int, default=None, help='Maximum number of sequences in orthogroup alignments')
28 parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, default=None, help='Minimum number of sequences in orthogroup alignments') 28 parser.add_argument('--min_orthogroup_size', dest='min_orthogroup_size', type=int, default=None, help='Minimum number of sequences in orthogroup alignments')
29 parser.add_argument('--remove_sequences', dest='remove_sequences', default=None, type=float, help='Remove sequences with gaps of') 29 parser.add_argument('--remove_sequences', dest='remove_sequences', default=None, type=float, help='Remove sequences with gaps of')