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)
# Misc functions
# ------------------------------------
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__ == "__main__":
# Get parameters
args = argParser()
fh = IO.mopen(args.ofname, 'w')
genome = FastaFile(args.genome)
for i, item in enumerate(IO.BioReader(args.ifname, args.ftype)):
try:
strand = item.strand
except:
strand = "+"
seq = item.getSeq(genome)
if len(seq) > 0:
print >> fh, '>' + (item.id != "NONAME" and item.id
or "item_" + str(i))
if args.linelength:
seq = seq.formatSeq(args.linelength)
if args.case == 'u':
seq = seq.upper()
elif args.case == 'l':
seq = seq.lower()
