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()