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)))
parser.add_argument('-H',
'--histogram_file',
help="Save score histograms to FILE")
parser.add_argument('-j',
'--nthreads',
help="Number of threads.",
type=int,
default=16)
args = parser.parse_args()
if args.top:
import psutil
hra = HiriseAssembly()
hra.load_assembly(args.infile)
hra.merge_masked_regions(debug=args.debug)
print(len(hra.layout_lines))
if len(hra.layout_lines) == 0:
print("#make trivial layout")
hra.make_trivial_layout_lines(debug=args.debug)
ces.set_exp_insert_size_dist_fit_params(hra.model_params)
model = ces.model
nbams = len(hra.bams)
inq = JoinableQueue(maxsize=0)
readers = []
for i in range(nbams):
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)
