from __future__ import division
from __future__ import print_function
from builtins import range
from past.utils import old_div
from hirise_assembly import HiriseAssembly
if __name__=="__main__":
import sys
import argparse
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-d','--debug',default=False ,action="store_true",help="Turn on debugging ouput")
parser.add_argument('-L','--layout',default=False ,help="A file containing a layout of contigs.")
parser.add_argument('-i','--infile',default=False ,help="Filename for serialised assembly input file.")
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)
if args.outfile:
f=open(args.outfile,"wt")
for contig in asf.contigs_iter():
f.write("{}\t{}\n".format(contig,asf.contig_length(contig)))
