def test_filter_reference_contigs(self):
ds2 = ReferenceSet(data.getRef())
self.assertEqual(len(list(ds2.refNames)), 59)
filt = Filters()
filt.addRequirement(id=[('==', 'E.faecalis.1')])
ds2.addFilters(filt)
self.assertEqual(str(ds2.filters), "( id == E.faecalis.1 )")
self.assertEqual(len(ds2.refNames), 1)
self.assertEqual(len(list(ds2.records)), 1)
ds2.disableFilters()
self.assertEqual(len(list(ds2.refNames)), 59)
self.assertEqual(len(list(ds2.records)), 59)
ds2.enableFilters()
self.assertEqual(len(list(ds2.refNames)), 1)
self.assertEqual(len(list(ds2.records)), 1)
def test_filter_reference_contigs(self):
ds2 = ReferenceSet(data.getRef())
self.assertEqual(len(list(ds2.refNames)), 59)
filt = Filters()
filt.addRequirement(id=[('==', 'E.faecalis.1')])
ds2.addFilters(filt)
self.assertEqual(str(ds2.filters),
"( id == E.faecalis.1 )")
self.assertEqual(len(ds2.refNames), 1)
self.assertEqual(len(list(ds2.records)), 1)
ds2.disableFilters()
self.assertEqual(len(list(ds2.refNames)), 59)
self.assertEqual(len(list(ds2.records)), 59)
ds2.enableFilters()
self.assertEqual(len(list(ds2.refNames)), 1)
self.assertEqual(len(list(ds2.records)), 1)
def test_loading_reference(self):
log.info('Opening Reference')
r = ReferenceSet(data.getRef()).toExternalFiles()[0]
log.info('Done Opening Reference')
log.info('Opening AlignmentSet')
d = AlignmentSet(data.getBam(), referenceFastaFname=r)
log.info('Done Opening AlignmentSet')
bfile = openIndexedAlignmentFile(data.getBam(), referenceFastaFname=r)
self.assertTrue(bfile.isReferenceLoaded)
for res in d.resourceReaders():
self.assertTrue(res.isReferenceLoaded)
aln = AlignmentSet(data.getBam())
aln.addReference(r)
for res in aln.resourceReaders():
self.assertTrue(res.isReferenceLoaded)
def test_loading_reference(self):
log.info('Opening Reference')
r = ReferenceSet(data.getRef()).toExternalFiles()[0]
log.info('Done Opening Reference')
log.info('Opening AlignmentSet')
d = AlignmentSet(data.getBam(), referenceFastaFname=r)
log.info('Done Opening AlignmentSet')
bfile = openIndexedAlignmentFile(data.getBam(),
referenceFastaFname=r)
self.assertTrue(bfile.isReferenceLoaded)
for res in d.resourceReaders():
self.assertTrue(res.isReferenceLoaded)
aln = AlignmentSet(data.getBam())
aln.addReference(r)
for res in aln.resourceReaders():
self.assertTrue(res.isReferenceLoaded)
def test_filter_reference_contigs(self):
ds2 = ReferenceSet(data.getRef())
assert len(list(ds2.refNames)) == 59
assert len(list(ds2.records)) == len(ds2.index)
filt = Filters()
filt.addRequirement(id=[('==', 'E.faecalis.1')])
ds2.addFilters(filt)
assert str(ds2.filters) == "( id == E.faecalis.1 )"
assert len(ds2.refNames) == 1
assert len(list(ds2.records)) == 1
assert len(list(ds2.records)) == len(ds2.index)
ds2.disableFilters()
assert len(list(ds2.refNames)) == 59
assert len(list(ds2.records)) == 59
assert len(list(ds2.records)) == len(ds2.index)
ds2.enableFilters()
assert len(list(ds2.refNames)) == 1
assert len(list(ds2.records)) == 1
assert len(list(ds2.records)) == len(ds2.index)