default=False, help="Filename for serialised assembly input file.") parser.add_argument('-f', '--fasta', default=False, help="Filename for original contigs fasta.") parser.add_argument( '-o', '--outfile', default=False, help= "Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking." ) args = parser.parse_args() if args.infile: asf = HiriseAssembly() asf.load_assembly(args.infile) asf.ocontig_fasta = args.fasta if args.outfile: outfasta = fastaWriter(args.outfile) for contig in asf.contigs_iter(): outfasta.next(contig) outfasta.write(asf.get_seq(contig)) outfasta.flush() outfasta.close()