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()
