comparison gene_family_classifier.py @ 154:36ed0037292a draft

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153:889d928f16b9

parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, help='Minimum taxa required in single copy orthogroup')
parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences')
parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences')
parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log')
parser.add_argument('--hmmscan_log', dest='hmmscan_log', default=None, help='hmmscan log file')
parser.add_argument('--output_ptortho', dest='output_ptortho', default=None, help='Output for orthogroups')
parser.add_argument('--output_ptortho_dir', dest='output_ptortho_dir', default=None, help='output_ptortho.files_path')
parser.add_argument('--output_ptorthocs', dest='output_ptorthocs', default=None, help='Output for orthogroups with corresponding coding sequences')
parser.add_argument('--output_ptorthocs_dir', dest='output_ptorthocs_dir', default=None, help='output_ptorthocs.files_path')
parser.add_argument('--output_ptsco', dest='output_ptsco', default=None, help='Output for single copy orthogroups')
parser.add_argument('--output_ptsco_dir', dest='output_ptsco_dir', default=None, help='output_ptsco.files_path')

args = parser.parse_args()

# Build the command line.
cmd = 'GeneFamilyClassifier'

        else:
            shutil.move(src_hmmscan_log, args.hmmscan_log)

# Handle orthogroups outputs.
if create_ortho_sequences:
    if create_corresponding_coding_sequences:
        out_file = args.output_ptorthocs
        orthogroups_fasta_dest_dir = args.output_ptorthocs_dir
        title = 'Orthogroups and corresponding coding sequences files'
    else:
        out_file = args.output_ptortho
        orthogroups_fasta_dest_dir = args.output_ptortho_dir
        title = 'Orthogroups files'
    orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
    utils.move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir)
    utils.write_html_output(out_file, title, orthogroups_fasta_dest_dir)

# Handle single copy orthogroup outputs.
if args.output_ptsco is not None:
    single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')
    single_copy_fasta_dest_dir = args.output_ptsco_dir
    title = 'Single copy orthogroups files'
    utils.move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir)
    utils.write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir)

154:36ed0037292a

parser.add_argument('--taxa_present', dest='taxa_present', type=int, default=0, help='Minimum taxa required in single copy orthogroup')
parser.add_argument('--orthogroup_fasta', dest='orthogroup_fasta', default=None, help='Flag to create orthogroup sequences')
parser.add_argument('--coding_sequences', dest='coding_sequences', default=None, help='Flag to create orthogroup coding sequences')
parser.add_argument('--save_hmmscan_log', dest='save_hmmscan_log', default=None, help='Flag to save the hmmscan log')
parser.add_argument('--hmmscan_log', dest='hmmscan_log', default=None, help='hmmscan log file')

args = parser.parse_args()

# Build the command line.
cmd = 'GeneFamilyClassifier'

        else:
            shutil.move(src_hmmscan_log, args.hmmscan_log)

# Handle orthogroups outputs.
if create_ortho_sequences:
    orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta')
    orthogroups_fasta_dest_dir = 'output_orthos_dir'
    if not os.path.isdir(orthogroups_fasta_dest_dir):
        os.makedirs(orthogroups_fasta_dest_dir)
    # Remove source direrctory so it won't break dataset collection handler.
    utils.move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir, remove_source_dir=True)

# Handle single copy orthogroup outputs.
if args.single_copy_custom is not None or args.single_copy_taxa != 0:
    single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta')
    single_copy_fasta_dest_dir = 'output_single_copy_fasta_dir'
    if not os.path.isdir(single_copy_fasta_dest_dir):
        os.makedirs(single_copy_fasta_dest_dir)
    # Remove source direrctory so it won't break dataset collection handler.
    utils.move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir, remove_source_dir=True)