join_spades_fastg_by_blast.py 文件源码

def require_commands():
    global 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 = 'python '+str(os.path.basename(__file__))+' -g input.fastg -f refernce.fasta'
    parser = OptionParser(usage=usage)
    parser.add_option('-g', dest='in_fastg_file', help='followed by your input fastg file')
    parser.add_option('-f', dest='reference_fa_base', help='followed by Fasta index format')
    parser.add_option('--keep-temp', dest='keep_temp', default=False, action='store_true', help='Choose to disable deleting temp files produced by blast and this script')
    parser.add_option('--bt', dest='blast_hits_threshold', default=0.60, help='Default: 0.60', type=float)
    parser.add_option('--max-gap', dest='max_gap_to_add', default=1500, help='Default: 1500', type=int)
    parser.add_option('--con-all', dest='connect_inner_contig', default=False, action='store_true', help='Choose to activate connecting all possible contigs. Default: False')
    parser.add_option('--depth', dest='depth_to_connect', default=1.0, help='Default: 1.0', type=float)
    # parser.add_option('--merge-overlaps', default=False, action='store_true', help='Choose to activate automatically merging overlapping contigs')
    # parser.add_option('--min-os', dest='min_overlap_similarity', default=0.9, help='The similarity threshold to merge overlapping contigs. Default: 0.9', type=float)
    # parser.add_option('--min-ol', dest='min_overlap_length', default=15, help='The length threshold to merge overlapping contigs. Default: 15', type=int)
    try:
        (options, args) = parser.parse_args()
    except Exception as e:
        sys.stdout.write('\n######################################'+str(e))
        sys.stdout.write('\n"-h" for more usage')
        exit()