#!/usr/bin/env python

import sys

from itertools import groupby,ifilter,izip_longest,count

from io import getNucmerAlignmentIterator

from cov import fillc, getMarkedRanges, getCoverageFromNucAlignments

if not len(sys.argv) == 4:

print "pb_uncovered.py <in.nuc.sc> <min_gap> <out_prefix>"

sys.exit(1)

fh = open(sys.argv[1])

COV_GAP_MIN = int(sys.argv[2])

fhist = open(sys.argv[3] + ".uncov.hist", "w")

freg = open(sys.argv[3] + ".uncov.regions", "w")

ftbases = open(sys.argv[3] + ".uncov.total.bases", "w")

pcov = [] #pct cov

total_bases = 0

total_uncovered_bases = 0

for pbname,alignments in groupby(getNucmerAlignmentIterator(fh), lambda x: x.sname):

a = list(alignments)

cov = getCoverageFromNucAlignments(a)

#mark the 0 coverage regions

zcov = map(lambda c: 1 if c == 0 else 0, cov)

#ranges with 0 coverage

zcov_ranges = getMarkedRanges(zcov)

#only look at the gaps larger than the min gap size

zcov_ranges_filt = filter(lambda (x,y) : y-x > COV_GAP_MIN ,zcov_ranges )

#write out the regions that pass filter to region file

freg.write("\t".join([pbname, " ".join(map(lambda t: "%d,%d" % t, zcov_ranges_filt))]) + "\n")

total_bases += a[0].slen

for rbeg,rend in zcov_ranges_filt:

total_uncovered_bases += rend - rbeg

pct_ranges = map(lambda (rb,re) : (int(float(rb)/(a[0].slen-1)*100),int(float(re)/(a[0].slen-1)*100)), zcov_ranges_filt)

for pr_b,pr_e in pct_ranges:

fillc(pcov,pr_b,pr_e)

ftbases.write("%d / %d = %f\n" % (total_uncovered_bases,total_bases, float(total_uncovered_bases)/total_bases))

#print nicely

map(lambda t: fhist.write("%d\t%d\n" % t), izip_longest(range(100),pcov,fillvalue=0))

fh.close()

fhist.close()

freg.close()

ftbases.close()