def cropGFF(gffs, options):
"""crop intervals in gff file."""
# read regions to crop with and convert intervals to intersectors
E.info("reading gff for cropping: started.")
other_gffs = GTF.iterator(IOTools.openFile(options.crop, "r"))
cropper = GTF.readAsIntervals(other_gffs)
ntotal = 0
for contig in cropper.keys():
intersector = bx.intervals.intersection.Intersecter()
for start, end in cropper[contig]:
intersector.add_interval(bx.intervals.Interval(start, end))
ntotal += 1
cropper[contig] = intersector
E.info("reading gff for cropping: finished.")
E.info("reading gff for cropping: %i contigs with %i intervals." %
(len(cropper), ntotal))
ninput, noutput, ncropped, ndeleted = 0, 0, 0, 0
# do the actual cropping
for gff in gffs:
ninput += 1
if gff.contig in cropper:
start, end = gff.start, gff.end
overlaps = cropper[gff.contig].find(start, end)
if overlaps:
l = end - start
a = numpy.ones(l)
for i in overlaps:
s = max(0, i.start - start)
e = min(l, i.end - start)
a[s:e] = 0
segments = Intervals.fromArray(a)
if len(segments) == 0:
ndeleted += 1
else:
ncropped += 1
for s, e in segments:
gff.start, gff.end = s + start, e + start
noutput += 1
options.stdout.write("%s\n" % gff)
continue
noutput += 1
options.stdout.write("%s\n" % gff)
if options.loglevel >= 1:
options.stdlog.write(
"# ninput=%i, noutput=%i, ncropped=%i, ndeleted=%i\n" %
(ninput, noutput, ncropped, ndeleted))
def cropGFF(gffs, options):
"""crop intervals in gff file."""
# read regions to crop with and convert intervals to intersectors
E.info("reading gff for cropping: started.")
other_gffs = GTF.iterator(IOTools.openFile(options.crop, "r"))
cropper = GTF.readAsIntervals(other_gffs)
ntotal = 0
for contig in cropper.keys():
intersector = bx.intervals.intersection.Intersecter()
for start, end in cropper[contig]:
intersector.add_interval(bx.intervals.Interval(start, end))
ntotal += 1
cropper[contig] = intersector
E.info("reading gff for cropping: finished.")
E.info("reading gff for cropping: %i contigs with %i intervals." %
(len(cropper), ntotal))
ninput, noutput, ncropped, ndeleted = 0, 0, 0, 0
# do the actual cropping
for gff in gffs:
ninput += 1
if gff.contig in cropper:
start, end = gff.start, gff.end
overlaps = cropper[gff.contig].find(start, end)
if overlaps:
l = end - start
a = numpy.ones(l)
for i in overlaps:
s = max(0, i.start - start)
e = min(l, i.end - start)
a[s:e] = 0
segments = Intervals.fromArray(a)
if len(segments) == 0:
ndeleted += 1
else:
ncropped += 1
for s, e in segments:
gff.start, gff.end = s + start, e + start
noutput += 1
options.stdout.write("%s\n" % gff)
continue
noutput += 1
options.stdout.write("%s\n" % gff)
if options.loglevel >= 1:
options.stdlog.write("# ninput=%i, noutput=%i, ncropped=%i, ndeleted=%i\n" % (
ninput, noutput, ncropped, ndeleted))
def testArray2(self):
"""test longer array."""
a = [1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1]
self.assertEqual(Intervals.fromArray(a), [(0, 3), (6, 9), (12, 15)])
self.assertEqual(Intervals.fromArray([not x for x in a]), [(3, 6),
(9, 12)])
def testArray1(self):
"""test simple array."""
a = [1, 1, 1, 0, 0, 0, 1, 1, 1]
self.assertEqual(Intervals.fromArray(a), [(0, 3), (6, 9)])
self.assertEqual(Intervals.fromArray([not x for x in a]), [(3, 6)])
def testEmpty(self):
"""test empty input."""
self.assertEqual(Intervals.fromArray([]), [])
def testArray2(self):
"""test longer array."""
a = [1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1]
self.assertEqual(Intervals.fromArray(a), [(0, 3), (6, 9), (12, 15)])
self.assertEqual(
Intervals.fromArray([not x for x in a]), [(3, 6), (9, 12)])
def testArray1(self):
"""test simple array."""
a = [1, 1, 1, 0, 0, 0, 1, 1, 1]
self.assertEqual(Intervals.fromArray(a), [(0, 3), (6, 9)])
self.assertEqual(Intervals.fromArray([not x for x in a]), [(3, 6)])
def testEmpty(self):
"""test empty input."""
self.assertEqual(Intervals.fromArray([]), [])
def cropGFF(gffs, filename_gff):
"""crop intervals in gff file."""
# read regions to crop with and convert intervals to intersectors
E.info("reading gff for cropping: started.")
other_gffs = GTF.iterator(IOTools.open_file(filename_gff, "r"))
cropper = GTF.readAsIntervals(other_gffs)
ntotal = 0
for contig in list(cropper.keys()):
intersector = quicksect.IntervalTree()
for start, end in cropper[contig]:
intersector.add(start, end)
ntotal += 1
cropper[contig] = intersector
E.info("reading gff for cropping: finished.")
E.info("reading gff for cropping: %i contigs with %i intervals." %
(len(cropper), ntotal))
ninput, noutput, ncropped, ndeleted = 0, 0, 0, 0
# do the actual cropping
for gff in gffs:
ninput += 1
if gff.contig in cropper:
start, end = gff.start, gff.end
overlaps = cropper[gff.contig].find(quicksect.Interval(start, end))
if overlaps:
l = end - start
a = numpy.ones(l)
for i in overlaps:
s = max(0, i.start - start)
e = min(l, i.end - start)
a[s:e] = 0
segments = Intervals.fromArray(a)
if len(segments) == 0:
ndeleted += 1
else:
ncropped += 1
for s, e in segments:
gff.start, gff.end = s + start, e + start
noutput += 1
yield (gff)
continue
noutput += 1
yield (gff)
E.info("ninput=%i, noutput=%i, ncropped=%i, ndeleted=%i" %
(ninput, noutput, ncropped, ndeleted))
