def test_split_by_contigs_presplit(self):
# Consumes too much memory for Jenkins
# Test to make sure the result of a split by contigs has an appropriate
# number of records (make sure filters are appropriately aggressive)
ds2 = DataSet(data.getXml(14))
bams = ds2.externalResources.resourceIds
assert len(bams) == 2
refwindows = ds2.refWindows
assert refwindows == [(0, 0, 224992)]
res1 = openIndexedAlignmentFile(bams[0][7:])
res2 = openIndexedAlignmentFile(bams[1][7:])
def count(iterable):
count = 0
for _ in iterable:
count += 1
return count
assert count(res1.readsInRange(*refwindows[0])) == 1409
assert count(res2.readsInRange(*refwindows[0])) == 1375
assert count(ds2.readsInRange(*refwindows[0])) == 2784
assert count(ds2.records) == 2784
ds2.disableFilters()
assert count(ds2.records) == 53552
assert ds2.countRecords() == 53552
def test_split_by_contigs_presplit(self):
# Consumes too much memory for Jenkins
# Test to make sure the result of a split by contigs has an appropriate
# number of records (make sure filters are appropriately aggressive)
ds2 = DataSet(data.getXml(15))
bams = ds2.externalResources.resourceIds
self.assertEqual(len(bams), 2)
refwindows = ds2.refWindows
self.assertEqual(refwindows, [(0, 0, 224992)])
res1 = openIndexedAlignmentFile(bams[0][7:])
res2 = openIndexedAlignmentFile(bams[1][7:])
def count(iterable):
count = 0
for _ in iterable:
count += 1
return count
self.assertEqual(count(res1.readsInRange(*refwindows[0])), 1409)
self.assertEqual(count(res2.readsInRange(*refwindows[0])), 1375)
self.assertEqual(count(ds2.readsInRange(*refwindows[0])), 2784)
self.assertEqual(count(ds2.records), 2784)
ds2.disableFilters()
self.assertEqual(count(ds2.records), 53552)
self.assertEqual(ds2.countRecords(), 53552)
def test_reads_in_range(self):
ds = DataSet(data.getBam())
refNames = ds.refNames
rn = refNames[15]
reads = ds.readsInRange(rn, 10, 100)
self.assertEqual(len(list(reads)), 10)
ds2 = DataSet(data.getBam(0))
reads = ds2.readsInRange("E.faecalis.1", 0, 1400)
self.assertEqual(len(list(reads)), 20)
lengths = ds.refLengths
for rname, rId in ds.refInfo('ID'):
rn = ds._idToRname(rId)
self.assertEqual(rname, rn)
rlen = lengths[rn]
self.assertEqual(len(list(ds.readsInReference(rn))),
len(list(ds.readsInReference(rId))))
self.assertEqual(len(list(ds.readsInRange(rn, 0, rlen))),
len(list(ds.readsInRange(rId, 0, rlen))))
def test_reads_in_range(self):
ds = DataSet(data.getBam())
refNames = ds.refNames
rn = refNames[15]
reads = ds.readsInRange(rn, 10, 100)
self.assertEqual(len(list(reads)), 10)
ds2 = DataSet(data.getBam(0))
reads = ds2.readsInRange("E.faecalis.1", 0, 1400)
self.assertEqual(len(list(reads)), 20)
lengths = ds.refLengths
for rname, rId in ds.refInfo('ID'):
rn = ds._idToRname(rId)
self.assertEqual(rname, rn)
rlen = lengths[rn]
self.assertEqual(len(list(ds.readsInReference(rn))),
len(list(ds.readsInReference(rId))))
self.assertEqual(len(list(ds.readsInRange(rn, 0, rlen))),
len(list(ds.readsInRange(rId, 0, rlen))))
def test_staggered_reads_in_range(self):
ds = DataSet(data.getXml(8))
refNames = ds.refNames
rn = 'B.vulgatus.5'
reads = list(ds.readsInRange(rn, 0, 10000))
ds2 = DataSet(data.getXml(11))
reads2 = list(ds2.readsInRange(rn, 0, 10000))
dsBoth = DataSet(data.getXml(8), data.getXml(11))
readsBoth = list(dsBoth.readsInRange(rn, 0, 10000))
self.assertEqual(len(reads), 2)
self.assertEqual(len(reads2), 5)
self.assertEqual(len(readsBoth), 7)
read_starts = (0, 1053)
for read, start in zip(reads, read_starts):
self.assertEqual(read.tStart, start)
read2_starts = (0, 0, 3, 3, 4)
for read, start in zip(reads2, read2_starts):
self.assertEqual(read.tStart, start)
readboth_starts = (0, 0, 0, 3, 3, 4, 1053)
for read, start in zip(readsBoth, readboth_starts):
self.assertEqual(read.tStart, start)
def test_staggered_reads_in_range(self):
ds = DataSet(data.getXml(8))
refNames = ds.refNames
rn = 'B.vulgatus.5'
reads = list(ds.readsInRange(rn, 0, 10000))
ds2 = DataSet(data.getXml(11))
reads2 = list(ds2.readsInRange(rn, 0, 10000))
dsBoth = DataSet(data.getXml(8), data.getXml(11))
readsBoth = list(dsBoth.readsInRange(rn, 0, 10000))
self.assertEqual(len(reads), 2)
self.assertEqual(len(reads2), 5)
self.assertEqual(len(readsBoth), 7)
read_starts = (0, 1053)
for read, start in zip(reads, read_starts):
self.assertEqual(read.tStart, start)
read2_starts = (0, 0, 3, 3, 4)
for read, start in zip(reads2, read2_starts):
self.assertEqual(read.tStart, start)
readboth_starts = (0, 0, 0, 3, 3, 4, 1053)
for read, start in zip(readsBoth, readboth_starts):
self.assertEqual(read.tStart, start)
def test_split_by_contigs_presplit(self):
# Consumes too much memory for Jenkins
# Test to make sure the result of a split by contigs has an appropriate
# number of records (make sure filters are appropriately aggressive)
ds2 = DataSet(data.getXml(15))
bams = ds2.externalResources.resourceIds
self.assertEqual(len(bams), 2)
refwindows = ds2.refWindows
self.assertEqual(refwindows, [(0, 0, 224992)])
res1 = openIndexedAlignmentFile(bams[0][7:])
res2 = openIndexedAlignmentFile(bams[1][7:])
def count(iterable):
count = 0
for _ in iterable:
count += 1
return count
self.assertEqual(count(res1.readsInRange(*refwindows[0])), 1409)
self.assertEqual(count(res2.readsInRange(*refwindows[0])), 1375)
self.assertEqual(count(ds2.readsInRange(*refwindows[0])), 2784)
self.assertEqual(count(ds2.records), 2784)
ds2.disableFilters()
self.assertEqual(count(ds2.records), 53552)
self.assertEqual(ds2.countRecords(), 53552)
