args = parser.parse_args()
if args.infile:
asf = HiriseAssembly()
asf.load_assembly(args.infile)
# asf = HiriseAssembly()
# asf.load_playout(args.infile)
breaks=[]
scores={}
for l in open(args.breaks):
if l[0]=="#": continue
#Scaffold102239 741 1379 5097 -5.421961663655971
scaffold,a,b,slen,score = l.strip().split()
a=int(a) #start
b=int(b) #end
# c=int(c) #lowpoint
score=float(score)
c=int((a+b)/2)
breaks.append((scaffold,a,b,c))
scores[scaffold,a,b,c]=score
# asf.add_breakpoints_ranges(breaks,debug=args.debug,scores=scores)
asf.add_breakpoints_ranges(breaks,debug=args.debug)
asf.validate()
if args.outfile: asf.save_assembly( args.outfile )
#
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.layout:
asf.load_playout(args.layout)
if args.outfile:
asf.save_assembly( args.outfile )
