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")
if not len(sys.argv) == 4:
print "gc_count.py reads.fa alignments.sc outprefix"
sys.exit(1)
rfh = open(sys.argv[1])
afh = open(sys.argv[2])
ofh = open(sys.argv[3]+".uncov.gc.bases","w")
reads = {}
for entry in fastaIterator(rfh):
reads[str(entry.name)] = str(entry.seq)
sys.stderr.write("Loaded reads\n")
alignmentIt = getNucmerAlignmentIterator(afh)
sys.stderr.write("Loaded Alignments\n");
counter = 0
for name,group in groupby(alignmentIt, lambda x: x.sname):
#build coverage vector
cov = getCoverageFromNucAlignments(group)
#mark the regions with 0 (no) coverage as 1 and change
#everything else to 0
cov_inv = map(lambda c: 1 if c == 0 else 0, cov)
#ranges with zero coverage
zero_cov_ranges = getMarkedRanges(cov_inv)
import sys
from io import getNucmerAlignmentIterator, nucRecordToString
from itertools import groupby
from operator import attrgetter
#dist from the end
#that is considered in the middle
END_CUTOFF = 200
if not len(sys.argv) == 2:
sys.exit("alignment_verify.py alignments.sc")
fh = open(sys.argv[1])
for pbname, alignments in groupby(getNucmerAlignmentIterator(fh), attrgetter("sname")):
al = list(alignments)
##if all alignments are to the same unitig
if all(map(lambda x: x.qname == al[0].qname , al)):
continue
for aln in al:
if (aln.qstart > END_CUTOFF and aln.qstart < (aln.qlen-END_CUTOFF)
and aln.qend > END_CUTOFF and aln.qend < (aln.qlen-END_CUTOFF)):
print nucRecordToString(aln)+"\tMIDDLE"
else:
print nucRecordToString(aln)
fh.close()
