Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.py @ 101:cd23ab8b617f draft

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Uploaded
author greg
date Mon, 27 Feb 2017 11:07:43 -0500
parents ba924b724a8d
children 55052911cac3
comparison
equal deleted inserted replaced
100:87d078898e14 101:cd23ab8b617f
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') 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')
28 parser.add_argument('--output_ptorthocs', dest='output_ptorthocs', default=None, help='Output for orthogroups with corresponding coding sequences') 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')
29 parser.add_argument('--output_ptsco', dest='output_ptsco', default=None, help='Output for single copy orthogroups') 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')
30 33
31 args = parser.parse_args() 34 args = parser.parse_args()
32 35
33 36
34 def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False): 37 def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False):
137 shutil.move(src_hmmscan_log, args.hmmscan_log) 140 shutil.move(src_hmmscan_log, args.hmmscan_log)
138 # Handle orthogroups outputs. 141 # Handle orthogroups outputs.
139 if create_ortho_sequences: 142 if create_ortho_sequences:
140 if create_corresponding_coding_sequences: 143 if create_corresponding_coding_sequences:
141 out_file = args.output_ptorthocs 144 out_file = args.output_ptorthocs
145 orthogroups_fasta_dest_dir = args.output_ptorthocs_dir
142 title = 'Orthogroups with corresponding coding sequences' 146 title = 'Orthogroups with corresponding coding sequences'
143 else: 147 else:
144 out_file = args.output_ptortho 148 out_file = args.output_ptortho
149 orthogroups_fasta_dest_dir = args.output_ptortho_dir
145 title = 'Orthogroups' 150 title = 'Orthogroups'
146 orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta') 151 orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
147 orthogroups_fasta_dest_dir = out_file.files_path
148 move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_src_dir) 152 move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_src_dir)
149 write_html_output(out_file, title, orthogroups_fasta_dest_dir) 153 write_html_output(out_file, title, orthogroups_fasta_dest_dir)
150 # Handle single copy orthogroup outputs. 154 # Handle single copy orthogroup outputs.
151 if args.output_ptsco is not None: 155 if args.output_ptsco is not None:
152 single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta') 156 single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')
153 single_copy_fasta_dest_dir = args.output_ptsco.files_path 157 single_copy_fasta_dest_dir = args.output_ptsco_dir
154 title = 'Single copy orthogroups' 158 title = 'Single copy orthogroups'
155 move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir) 159 move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir)
156 write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir) 160 write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir)