Mercurial > repos > greg > plant_tribes_gene_family_classifier

comparison gene_family_classifier.py @ 3:3e10a2683769 draft

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author greg
date Mon, 30 Oct 2017 09:52:34 -0400
parents f8603464bea7
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2:8ec75782a05b 3:3e10a2683769
22 parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, help='Minimum taxa required in single copy orthogroup') 22 parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, help='Minimum taxa required in single copy orthogroup')
23 parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences') 23 parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences')
24 parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences') 24 parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences')
25 parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log') 25 parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log')
26 parser.add_argument('--hmmscan_log', dest='hmmscan_log', default=None, help='hmmscan log file') 26 parser.add_argument('--hmmscan_log', dest='hmmscan_log', default=None, help='hmmscan log file')
27 parser.add_argument('--output_ptortho', dest='output_ptortho', default=None, help='Output for orthogroups')
28 parser.add_argument('--output_ptortho_dir', dest='output_ptortho_dir', default=None, help='output_ptortho.files_path')
29 parser.add_argument('--output_ptorthocs', dest='output_ptorthocs', default=None, help='Output for orthogroups with corresponding coding sequences')
30 parser.add_argument('--output_ptorthocs_dir', dest='output_ptorthocs_dir', default=None, help='output_ptorthocs.files_path')
31 parser.add_argument('--output_ptsco', dest='output_ptsco', default=None, help='Output for single copy orthogroups')
32 parser.add_argument('--output_ptsco_dir', dest='output_ptsco_dir', default=None, help='output_ptsco.files_path')
33 27
34 args = parser.parse_args() 28 args = parser.parse_args()
35 29
36 # Build the command line. 30 # Build the command line.
37 cmd = 'GeneFamilyClassifier' 31 cmd = 'GeneFamilyClassifier'
72 else: 66 else:
73 shutil.move(src_hmmscan_log, args.hmmscan_log) 67 shutil.move(src_hmmscan_log, args.hmmscan_log)
74 68
75 # Handle orthogroups outputs. 69 # Handle orthogroups outputs.
76 if create_ortho_sequences: 70 if create_ortho_sequences:
77 if create_corresponding_coding_sequences:
78 out_file = args.output_ptorthocs
79 orthogroups_fasta_dest_dir = args.output_ptorthocs_dir
80 title = 'Orthogroups and corresponding coding sequences files'
81 else:
82 out_file = args.output_ptortho
83 orthogroups_fasta_dest_dir = args.output_ptortho_dir
84 title = 'Orthogroups files'
85 orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta') 71 orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
86 utils.move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir) 72 orthogroups_fasta_dest_dir = 'output_orthogroups_fasta_dir'
87 utils.write_html_output(out_file, title, orthogroups_fasta_dest_dir) 73 if not os.path.isdir(orthogroups_fasta_dest_dir):
74 os.makedirs(orthogroups_fasta_dest_dir)
75 # Remove source direrctory so it won't break dataset collection handler.
76 utils.move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir, remove_source_dir=True)
88 77
89 # Handle single copy orthogroup outputs. 78 # Handle single copy orthogroup outputs.
90 if args.output_ptsco is not None: 79 if args.single_copy_custom is not None or args.single_copy_taxa != 0:
91 single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta') 80 single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')
92 single_copy_fasta_dest_dir = args.output_ptsco_dir 81 single_copy_fasta_dest_dir = 'output_single_copy_fasta_dir'
93 title = 'Single copy orthogroups files' 82 if not os.path.isdir(single_copy_fasta_dest_dir):
94 utils.move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir) 83 os.makedirs(single_copy_fasta_dest_dir)
95 utils.write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir) 84 # Remove source direrctory so it won't break dataset collection handler.
85 utils.move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir, remove_source_dir=True)