Mercurial > repos > greg > gene_family_classifier
comparison gene_family_classifier.py @ 133:b2ae23e484e8 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 11 Apr 2017 14:24:23 -0400 |
| parents | 656614635ebf |
| children | 07bf26b7a1ab |
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| 132:169504db8e43 | 133:b2ae23e484e8 |
|---|---|
| 10 BUFF_SIZE = 1048576 | 10 BUFF_SIZE = 1048576 |
| 11 OUTPUT_DIR = 'geneFamilyClassification_dir' | 11 OUTPUT_DIR = 'geneFamilyClassification_dir' |
| 12 | 12 |
| 13 parser = argparse.ArgumentParser() | 13 parser = argparse.ArgumentParser() |
| 14 parser.add_argument('--input', dest='input', help="Input dataset") | 14 parser.add_argument('--input', dest='input', help="Input dataset") |
| 15 parser.add_argument('--scaffold', dest='scaffold', default='mode', help='Orthogroups or gene families proteins scaffold') | 15 parser.add_argument('--scaffold', dest='scaffold', help='Orthogroups or gene families proteins scaffold') |
| 16 parser.add_argument('--method', dest='method', help='Protein clustering method') | 16 parser.add_argument('--method', dest='method', help='Protein clustering method') |
| 17 parser.add_argument('--classifier', dest='classifier', help='Protein classification method') | 17 parser.add_argument('--classifier', dest='classifier', help='Protein classification method') |
| 18 parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files') | 18 parser.add_argument('--config_dir', dest='config_dir', help='Directory containing default configuration files') |
| 19 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') | 19 parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of threads to use for execution') |
| 20 parser.add_argument('--super_orthogroups', dest='super_orthogroups', default=None, help='Super orthogroups clustering specification') | 20 parser.add_argument('--super_orthogroups', dest='super_orthogroups', default=None, help='Super orthogroups clustering specification') |
| 21 parser.add_argument('--single_copy_custom', dest='single_copy_custom', default=None, help='Custom single copy orthogroup configuration') | 21 parser.add_argument('--single_copy_custom', dest='single_copy_custom', default=None, help='Custom single copy orthogroup configuration') |
| 22 parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=None, help='"Minimum single copy taxa required in orthogroup') | 22 parser.add_argument('--single_copy_taxa', dest='single_copy_taxa', type=int, default=0, help='"Minimum single copy taxa required in orthogroup') |
| 23 parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=None, help='Minimum taxa required in single copy orthogroup') | 23 parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, help='Minimum taxa required in single copy orthogroup') |
| 24 parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences') | 24 parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences') |
| 25 parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences') | 25 parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences') |
| 26 parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log') | 26 parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log') |
| 27 parser.add_argument('--hmmscan_log', dest='hmmscan_log', default=None, help='hmmscan log file') | 27 parser.add_argument('--hmmscan_log', dest='hmmscan_log', default=None, help='hmmscan log file') |
| 28 parser.add_argument('--output_ptortho', dest='output_ptortho', default=None, help='Output for orthogroups') | 28 parser.add_argument('--output_ptortho', dest='output_ptortho', default=None, help='Output for orthogroups') |
| 45 cmd += ' --num_threads %d' % args.num_threads | 45 cmd += ' --num_threads %d' % args.num_threads |
| 46 if args.super_orthogroups is not None: | 46 if args.super_orthogroups is not None: |
| 47 cmd += ' --super_orthogroups %s' % args.super_orthogroups | 47 cmd += ' --super_orthogroups %s' % args.super_orthogroups |
| 48 if args.single_copy_custom is not None: | 48 if args.single_copy_custom is not None: |
| 49 cmd += ' --single_copy_custom %s' % args.single_copy_custom | 49 cmd += ' --single_copy_custom %s' % args.single_copy_custom |
| 50 if args.single_copy_taxa is not None: | 50 if args.single_copy_taxa > 0: |
| 51 cmd += ' --single_copy_taxa %d' % args.single_copy_taxa | 51 cmd += ' --single_copy_taxa %d' % args.single_copy_taxa |
| 52 if args.taxa_present is not None: | 52 if args.taxa_present > 0: |
| 53 cmd += ' --taxa_present %d' % args.taxa_present | 53 cmd += ' --taxa_present %d' % args.taxa_present |
| 54 if args.orthogroup_fasta is None: | 54 if args.orthogroup_fasta is None: |
| 55 create_ortho_sequences = False | 55 create_ortho_sequences = False |
| 56 else: | 56 else: |
| 57 create_ortho_sequences = True | 57 create_ortho_sequences = True |