Пример #1
0
        sys.exit(p.print_help())
    args = p.parse_args()
    return args

# ------------------------------------
# Classes
# ------------------------------------

# ------------------------------------
# Main
# ------------------------------------

if __name__=="__main__":
    # Get parameters
    args=argParser()
    fh = IO.mopen(args.ofname, 'w')
    lastbed = Bed("chr1\t0\t0")
    cnt = 0 # count of unique items
    for item in IO.BioReader(args.ifname,args.ftype):
        if item.chrom == lastbed.chrom and item.start == lastbed.start and item.stop == lastbed.stop:
            if args.names == 'c':
                lastbed.id += ";"+item.id
        else:
            if lastbed.stop !=0:
                cnt += 1
                if args.names == 'n':
                    lastbed.id = str(cnt)
                elif args.names == 'p':
                    lastbed.id = args.prefix+"_"+str(cnt)
                print >> fh, lastbed
Пример #2
0
                   required=False,
                   help='Output file name. Default is "stdout".')
    if len(sys.argv) == 1:
        sys.exit(p.print_help())
    args = p.parse_args()
    return args


# ------------------------------------
# Classes
# ------------------------------------

# ------------------------------------
# Main
# ------------------------------------

if __name__ == "__main__":
    args = argParser()
    fh = IO.mopen(args.ofname, 'w')
    # Fasta file
    fa = FastaFile(args.ifname)
    f = IO.mopen(args.names)
    for faid in f:
        faid = faid.rstrip()
        seq = fa.getSeq(faid)
        print >> fh, ">" + faid
        print >> fh, seq.formatSeq()
    fa.close()
    IO.mclose(f)
    IO.mclose(fh)
Пример #3
0
    args = p.parse_args()
    return args


# ------------------------------------
# Classes
# ------------------------------------

# ------------------------------------
# Main
# ------------------------------------

if __name__ == "__main__":
    # Get parameters
    args = argParser()
    fh = IO.mopen(args.ofname, 'w')
    lastbed = Bed("chr1\t0\t0")
    cnt = 0  # count of unique items
    for item in IO.BioReader(args.ifname, args.ftype):
        if item.chrom == lastbed.chrom and item.start == lastbed.start and item.stop == lastbed.stop:
            if args.names == 'c':
                lastbed.id += ";" + item.id
        else:
            if lastbed.stop != 0:
                cnt += 1
                if args.names == 'n':
                    lastbed.id = str(cnt)
                elif args.names == 'p':
                    lastbed.id = args.prefix + "_" + str(cnt)
                print >> fh, lastbed
Пример #4
0
    p.add_argument("-n","--names",dest='names',type=str,metavar="names.lst",required=True,help='A file with sequence names. Can be "stdin".')
    p.add_argument("-o","--output",dest='ofname',type=str, default="stdout", metavar="output.fa",required=False,help='Output file name. Default is "stdout".')
    if len(sys.argv)==1:
        sys.exit(p.print_help())
    args = p.parse_args()
    return args

# ------------------------------------
# Classes
# ------------------------------------

# ------------------------------------
# Main
# ------------------------------------

if __name__=="__main__":
    args = argParser()
    fh = IO.mopen(args.ofname, 'w')
    # Fasta file
    fa = FastaFile(args.ifname)
    f = IO.mopen(args.names)
    for faid in f:
        faid=faid.rstrip()
        seq=fa.getSeq(faid)
        print >> fh, ">"+faid
        print >> fh, seq.formatSeq()
    fa.close()
    IO.mclose(f)
    IO.mclose(fh)