from builtins import range
from past.utils import old_div
from hirise_assembly import HiriseAssembly
# import struct
# import hashlib
import re
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("-q", "--mapq", default=55, type=float, help="Minimum map quality threshold.")
parser.add_argument("-i", "--infile", default=False, help="Filename for serialised assembly input file.")
parser.add_argument("-o", "--outfile", default=False, help="Filename for bedfile output.")
args = parser.parse_args()
if args.infile:
hra = HiriseAssembly()
hra.load_assembly(args.infile)
if args.outfile:
of = open(args.outfile, "wt")
else:
of = sys.stdout
hra.read_deserts(mapq=55, outfile=of, min_len=1000)
from __future__ import print_function
from builtins import range
from past.utils import old_div
from hirise_assembly import HiriseAssembly
#import struct
#import hashlib
import re
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('-q','--mapq',default=55, type=float,help="Minimum map quality threshold.")
parser.add_argument('-i','--infile',default=False,help="Filename for serialised assembly input file.")
parser.add_argument('-o','--outfile',default=False,help="Filename for bedfile output.")
args = parser.parse_args()
if args.infile:
hra = HiriseAssembly()
hra.load_assembly(args.infile)
if args.outfile:
of=open(args.outfile,"wt")
else:
of=sys.stdout
hra.read_deserts(mapq=55,outfile=of,min_len=1000)
