def test_subreadset_consolidate(self):
log.debug("Test methods directly")
aln = SubreadSet(data.getXml(10), data.getXml(13))
self.assertEqual(len(aln.toExternalFiles()), 2)
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'merged.bam')
consolidateBams(aln.toExternalFiles(), outfn, filterDset=aln)
self.assertTrue(os.path.exists(outfn))
consAln = SubreadSet(outfn)
self.assertEqual(len(consAln.toExternalFiles()), 1)
for read1, read2 in zip(sorted(list(aln)), sorted(list(consAln))):
self.assertEqual(read1, read2)
self.assertEqual(len(aln), len(consAln))
log.debug("Test through API")
aln = SubreadSet(data.getXml(10), data.getXml(13))
self.assertEqual(len(aln.toExternalFiles()), 2)
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'merged.bam')
aln.consolidate(outfn)
self.assertTrue(os.path.exists(outfn))
self.assertEqual(len(aln.toExternalFiles()), 1)
nonCons = SubreadSet(data.getXml(10), data.getXml(13))
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(aln), len(nonCons))
def test_subreadset_consolidate(self):
log.debug("Test through API")
aln = SubreadSet(data.getXml(10), data.getXml(13))
self.assertEqual(len(aln.toExternalFiles()), 2)
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'merged.bam')
aln.consolidate(outfn)
self.assertTrue(os.path.exists(outfn))
self.assertEqual(len(aln.toExternalFiles()), 1)
nonCons = SubreadSet(data.getXml(10), data.getXml(13))
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(aln), len(nonCons))
def test_subreadset_consolidate(self):
log.debug("Test through API")
aln = SubreadSet(data.getXml(9), data.getXml(12))
assert len(aln.toExternalFiles()) == 2
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'merged.bam')
aln.consolidate(outfn)
assert os.path.exists(outfn)
assert len(aln.toExternalFiles()) == 1
# lets make sure we're not getting extra entries:
assert len(aln.externalResources) == 1
assert len(aln.externalResources[0].indices) == 2
nonCons = SubreadSet(data.getXml(9), data.getXml(12))
assert len(nonCons.toExternalFiles()) == 2
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
assert read1 == read2
assert len(aln) == len(nonCons)
def test_subreadset_consolidate(self):
log.debug("Test through API")
aln = SubreadSet(data.getXml(10), data.getXml(13))
self.assertEqual(len(aln.toExternalFiles()), 2)
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
outfn = os.path.join(outdir, 'merged.bam')
aln.consolidate(outfn)
self.assertTrue(os.path.exists(outfn))
self.assertEqual(len(aln.toExternalFiles()), 1)
# lets make sure we're not getting extra entries:
self.assertEqual(len(aln.externalResources), 1)
self.assertEqual(len(aln.externalResources[0].indices), 2)
nonCons = SubreadSet(data.getXml(10), data.getXml(13))
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(aln), len(nonCons))
