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
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)
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
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)
