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_alignmentset_consolidate(self):
log.debug("Test methods directly")
aln = AlignmentSet(data.getXml(12))
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 = AlignmentSet(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 = AlignmentSet(data.getXml(12))
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 = AlignmentSet(data.getXml(12))
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))
log.debug("Test with cheap filter")
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
aln.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
self.assertEqual(len(list(aln)), 7)
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 = AlignmentSet(data.getXml(12))
nonCons.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(list(aln)), len(list(nonCons)))
log.debug("Test with not refname filter")
# This isn't trivial with bamtools
"""
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
aln.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
self.assertEqual(len(list(aln)), 7)
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 = AlignmentSet(data.getXml(12))
nonCons.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(list(aln)), len(list(nonCons)))
"""
log.debug("Test with expensive filter")
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
aln.filters.addRequirement(accuracy=[('>', '.85')])
self.assertEqual(len(list(aln)), 174)
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 = AlignmentSet(data.getXml(12))
nonCons.filters.addRequirement(accuracy=[('>', '.85')])
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(list(aln)), len(list(nonCons)))
log.debug("Test cli")
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
datafile = os.path.join(outdir, "merged.bam")
xmlfile = os.path.join(outdir, "merged.xml")
cmd = "dataset.py consolidate {i} {d} {x}".format(i=data.getXml(12),
d=datafile,
x=xmlfile)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)
def test_alignmentset_consolidate(self):
log.debug("Test methods directly")
aln = AlignmentSet(data.getXml(12))
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,
useTmp=False)
self.assertTrue(os.path.exists(outfn))
consAln = AlignmentSet(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 methods directly in tmp")
aln = AlignmentSet(data.getXml(12))
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,
useTmp=True)
self.assertTrue(os.path.exists(outfn))
consAln = AlignmentSet(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 = AlignmentSet(data.getXml(12))
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 = AlignmentSet(data.getXml(12))
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))
# Test that it is a valid xml:
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
datafile = os.path.join(outdir, "apimerged.bam")
xmlfile = os.path.join(outdir, "apimerged.xml")
log.debug(xmlfile)
aln.write(xmlfile)
log.debug("Test with cheap filter")
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
aln.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
self.assertEqual(len(list(aln)), 7)
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 = AlignmentSet(data.getXml(12))
nonCons.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(list(aln)), len(list(nonCons)))
log.debug("Test with not refname filter")
# This isn't trivial with bamtools
"""
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
aln.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
self.assertEqual(len(list(aln)), 7)
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 = AlignmentSet(data.getXml(12))
nonCons.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(list(aln)), len(list(nonCons)))
"""
log.debug("Test with expensive filter")
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
aln.filters.addRequirement(accuracy=[('>', '.85')])
self.assertEqual(len(list(aln)), 174)
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 = AlignmentSet(data.getXml(12))
nonCons.filters.addRequirement(accuracy=[('>', '.85')])
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(list(aln)), len(list(nonCons)))
def test_alignmentset_consolidate(self):
log.debug("Test methods directly")
aln = AlignmentSet(data.getXml(12))
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 = AlignmentSet(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 = AlignmentSet(data.getXml(12))
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 = AlignmentSet(data.getXml(12))
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))
# Test that it is a valid xml:
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
datafile = os.path.join(outdir, "apimerged.bam")
xmlfile = os.path.join(outdir, "apimerged.xml")
log.debug(xmlfile)
aln.write(xmlfile)
log.debug("Test with cheap filter")
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
aln.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
self.assertEqual(len(list(aln)), 7)
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 = AlignmentSet(data.getXml(12))
nonCons.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(list(aln)), len(list(nonCons)))
log.debug("Test with not refname filter")
# This isn't trivial with bamtools
"""
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
aln.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
self.assertEqual(len(list(aln)), 7)
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 = AlignmentSet(data.getXml(12))
nonCons.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(list(aln)), len(list(nonCons)))
"""
log.debug("Test with expensive filter")
aln = AlignmentSet(data.getXml(12))
self.assertEqual(len(list(aln)), 177)
aln.filters.addRequirement(accuracy=[('>', '.85')])
self.assertEqual(len(list(aln)), 174)
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 = AlignmentSet(data.getXml(12))
nonCons.filters.addRequirement(accuracy=[('>', '.85')])
self.assertEqual(len(nonCons.toExternalFiles()), 2)
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
self.assertEqual(read1, read2)
self.assertEqual(len(list(aln)), len(list(nonCons)))
log.debug("Test cli")
outdir = tempfile.mkdtemp(suffix="dataset-unittest")
datafile = os.path.join(outdir, "merged.bam")
xmlfile = os.path.join(outdir, "merged.xml")
cmd = "dataset consolidate {i} {d} {x}".format(i=data.getXml(12),
d=datafile,
x=xmlfile)
log.debug(cmd)
o, r, m = backticks(cmd)
self.assertEqual(r, 0)