rm_low_coverage_duplicated_contigs.py 文件源码

def require_options():
    try:
        # python3
        blast_in_path = subprocess.getstatusoutput('blastn')
    except AttributeError:
        # python2
        blast_in_path = commands.getstatusoutput('blastn')
    if blast_in_path[0] == 32512:
        sys.stdout.write('\nError: blastn not in the path!')
        exit()
    try:
        # python3
        makeblastdb_in_path = subprocess.getstatusoutput('makeblastdb')
    except AttributeError:
        # python2
        makeblastdb_in_path = commands.getstatusoutput('makeblastdb')
    if makeblastdb_in_path[0] == 32512:
        sys.stdout.write('\nError: makeblastdb not in the path!')
        exit()
    usage = "Usage: rm_low_coverage_duplicated_contigs.py *.fastg"
    parser = OptionParser(usage=usage)
    parser.add_option('--cov-t', dest='coverage_threshold', default=0.12,
                      help='With ratio (coverage of query/coverage of subject) below which, '
                           'the query would be exposed to discarded. Default: 0.12')
    parser.add_option('--len-t', dest='length_threshold', default=0.9,
                      help='With overlap (length of hit of query/ length of query) above which, '
                           'the query would be exposed to discarded. Default: 0.9')
    parser.add_option('--blur', dest='blur_bases', default=False, action='store_true',
                      help='Replace hit low-coverage bases with N.')
    parser.add_option('--keep-temp', dest='keep_temp', default=False, action='store_true',
                      help='Keep temp blast files.')
    parser.add_option('-o', dest='output',
                      help='Output file. Default: *.purified.fastg')
    parser.add_option('-t', '--threads', dest="threads", default=4, type=int,
                      help="Threads of blastn.")
    options, args = parser.parse_args()
    if not args:
        parser.print_help()
        sys.stdout.write('\n######################################\nERROR: Insufficient REQUIRED arguments!\n\n')
        exit()
    return options, args