def _count(self, filename, idx):
'''count filename against idx.'''
overlapping_genes = set()
genes = set()
# iterate over exons
infile = IOTools.openFile(filename, "r")
it = Bed.bed_iterator(infile)
nexons, nexons_overlapping = 0, 0
nbases, nbases_overlapping = 0, 0
for this in it:
nexons += 1
nbases += this.end - this.start
try:
intervals = list(
idx[this.contig].find(max(0, this.start), this.end))
except KeyError:
continue
except Exception, msg:
raise Exception(
"error while processing %s, msg=%s" % (filename, msg))
if len(intervals) == 0:
continue
nexons_overlapping += 1
start, end = this.start, this.end
counts = numpy.zeros(end - start, numpy.int)
for other_start, other_end, other_value in intervals:
for x in range(max(start, other_start) - start, min(end, other_end) - start):
counts[x] += 1
nbases_overlapping += sum([1 for x in counts if x > 0])
def _count(self, filename, idx):
'''count filename against idx.'''
overlapping_genes = set()
genes = set()
# iterate over exons
infile = IOTools.openFile(filename, "r")
it = Bed.bed_iterator(infile)
nexons, nexons_overlapping = 0, 0
nbases, nbases_overlapping = 0, 0
for this in it:
nexons += 1
nbases += this.end - this.start
try:
intervals = list(idx[this.contig].find(max(0, this.start),
this.end))
except KeyError:
continue
except Exception as msg:
raise Exception("error while processing %s, msg=%s" %
(filename, msg))
if len(intervals) == 0:
continue
nexons_overlapping += 1
start, end = this.start, this.end
counts = numpy.zeros(end - start, numpy.int)
for other_start, other_end, other_value in intervals:
for x in range(
max(start, other_start) - start,
min(end, other_end) - start):
counts[x] += 1
nbases_overlapping += sum([1 for x in counts if x > 0])
infile.close()
return nexons, nexons_overlapping, nbases, nbases_overlapping
