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)
# ------------------------------------
# Misc functions
# ------------------------------------
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__=="__main__":
# Get parameters
args=argParser()
fh = IO.mopen(args.ofname)
genome=FastaFile(args.genome)
for i,item in enumerate(IO.BioReader(args.ifname,args.ftype)):
try:
strand = item.strand
except:
strand = "+"
seq=genome.getSeq(item.chrom,item.start,item.stop,strand)
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()
def ReadIntervals(bedfile):
intervals = []
for tbed in IO.ColumnReader(sys.argv[1], ftype="bed"):
intervals.append(tbed)
return intervals