def test_readFasta(self):
f = FastaReader(data.getFasta())
entries = list(f)
assert_equal(48, len(entries))
assert_equal("ref000001|EGFR_Exon_2", entries[0].header)
assert_equal("TTTCTTCCAGTTTGCCAAGGCACGAGTAACAAGCTCACGCAGTTGGGCACTTT"
"TGAAGATCATTTTCTCAGCCTCCAGAGGATGTTCAATAACTGTGAGGTGGTCC"
"TTGGGAATTTGGAAATTACCTATGTGCAGAGGAATTATGATCTTTCCTTCTTA"
"AAGGTTGGTGACTTTGATTTTCCT",
entries[0].sequence)
def test_readFasta(self):
f = FastaReader(data.getFasta())
entries = list(f)
assert_equal(48, len(entries))
assert_equal("ref000001|EGFR_Exon_2", entries[0].name)
assert_equal("TTTCTTCCAGTTTGCCAAGGCACGAGTAACAAGCTCACGCAGTTGGGCACTTT"
"TGAAGATCATTTTCTCAGCCTCCAGAGGATGTTCAATAACTGTGAGGTGGTCC"
"TTGGGAATTTGGAAATTACCTATGTGCAGAGGAATTATGATCTTTCCTTCTTA"
"AAGGTTGGTGACTTTGATTTTCCT",
entries[0].sequence)
assert_equal("e3912e9ceacd6538ede8c1b2adda7423",
entries[0].md5)
def test_merged_contigset(self):
fn = tempfile.NamedTemporaryFile(suffix=".contigset.xml").name
with ContigSet(upstreamData.getLambdaFasta(),
upstreamData.getFasta()) as cset:
self.assertEqual(len(list(cset)), 49)
self.assertEqual(len(cset), 49)
cset.consolidate()
cset.write(fn)
log.debug("Writing to {f}".format(f=fn))
self.assertEqual(len(list(cset)), 49)
self.assertEqual(len(cset), 49)
with ContigSet(fn) as cset:
self.assertEqual(len(list(cset)), 49)
self.assertEqual(len(cset), 49)
def setup(self):
self.fastaPath = data.getFasta()
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)))
log.debug("Test with one reference")
aln = AlignmentSet(data.getXml(12))
reference = upstreamData.getFasta()
aln.externalResources[0].reference = reference
nonCons = aln.copy()
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))
self.assertEqual(aln.externalResources[0].reference, reference)
log.debug("Test with two references")
aln = AlignmentSet(data.getXml(12))
reference = upstreamData.getFasta()
for extRes in aln.externalResources:
extRes.reference = reference
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))
self.assertEqual(aln.externalResources[0].reference, reference)
def test_alignmentset_consolidate(self):
log.debug("Test through API")
aln = AlignmentSet(data.getXml(11))
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
nonCons = AlignmentSet(data.getXml(11))
assert len(nonCons.toExternalFiles()) == 2
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
assert read1 == read2
assert 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(11))
assert len(list(aln)) == 177
aln.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
assert len(list(aln)) == 7
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
nonCons = AlignmentSet(data.getXml(11))
nonCons.filters.addRequirement(rname=[('=', 'B.vulgatus.5')])
assert len(nonCons.toExternalFiles()) == 2
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
assert read1 == read2
assert len(list(aln)) == len(list(nonCons))
log.debug("Test with not refname filter")
# This isn't trivial with bamtools
"""
aln = AlignmentSet(data.getXml(11))
assert len(list(aln)) == 177
aln.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
assert len(list(aln)) == 7
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
nonCons = AlignmentSet(data.getXml(11))
nonCons.filters.addRequirement(rname=[('!=', 'B.vulgatus.5')])
assert len(nonCons.toExternalFiles()) == 2
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
assert read1 == read2
assert len(list(aln)) == len(list(nonCons))
"""
log.debug("Test with expensive filter")
aln = AlignmentSet(data.getXml(11))
assert len(list(aln)) == 177
aln.filters.addRequirement(accuracy=[('>', '.85')])
assert len(list(aln)) == 174
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
nonCons = AlignmentSet(data.getXml(11))
nonCons.filters.addRequirement(accuracy=[('>', '.85')])
assert len(nonCons.toExternalFiles()) == 2
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
assert read1 == read2
assert len(list(aln)) == len(list(nonCons))
log.debug("Test with one reference")
aln = AlignmentSet(data.getXml(11))
reference = upstreamData.getFasta()
aln.externalResources[0].reference = reference
nonCons = aln.copy()
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
#nonCons = AlignmentSet(data.getXml(11))
assert len(nonCons.toExternalFiles()) == 2
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
assert read1 == read2
assert len(aln) == len(nonCons)
assert aln.externalResources[0].reference == reference
log.debug("Test with two references")
aln = AlignmentSet(data.getXml(11))
reference = upstreamData.getFasta()
for extRes in aln.externalResources:
extRes.reference = reference
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
#nonCons = AlignmentSet(data.getXml(11))
assert len(nonCons.toExternalFiles()) == 2
for read1, read2 in zip(sorted(list(aln)), sorted(list(nonCons))):
assert read1 == read2
assert len(aln) == len(nonCons)
assert aln.externalResources[0].reference == reference
class TestIndexedFastaReader:
FASTAPATH = data.getFasta()
def testIteration(self):
ft = IndexedFastaReader(self.FASTAPATH)
fr = FastaReader(self.FASTAPATH)
ftContigs = list(ft)
frContigs = list(fr)
assert len(frContigs) == len(ftContigs)
assert 48 == len(ftContigs)
for ftC, frC in zip(ftContigs, frContigs):
assert frC.header == ftC.header
assert frC.sequence == ftC.sequence[:]
# Unlike FastaReader, IndexedFastaReader iteration is repeatable.
assert 48 == len(list(ft))
def testAccessByName(self):
ft = IndexedFastaReader(self.FASTAPATH)
r000021 = ft["ref000021|EGFR_Exon_22\tMetadataTest"]
assert "ref000021|EGFR_Exon_22\tMetadataTest" == r000021.header
assert "ref000021|EGFR_Exon_22" == r000021.id
assert "MetadataTest" == r000021.comment
assert ("CACTGCCTCATCTCTCACCATCCCAAGGTGCCTATCAAGTGGATGGCATTGGAATCAATT"
"TTACACAGAATCTATACCCACCAGAGTGATGTCTGGAGCTACGGTGAGTCATAATCCTGA"
"TGCTAATGAGTTTGTACTGAGGCCAAGCTGG") == r000021.sequence[:]
def testAccessById(self):
ft = IndexedFastaReader(self.FASTAPATH)
r000021 = ft["ref000021|EGFR_Exon_22"]
assert "ref000021|EGFR_Exon_22\tMetadataTest" == r000021.header
assert "ref000021|EGFR_Exon_22" == r000021.id
assert "MetadataTest" == r000021.comment
assert ("CACTGCCTCATCTCTCACCATCCCAAGGTGCCTATCAAGTGGATGGCATTGGAATCAATT"
"TTACACAGAATCTATACCCACCAGAGTGATGTCTGGAGCTACGGTGAGTCATAATCCTGA"
"TGCTAATGAGTTTGTACTGAGGCCAAGCTGG") == r000021.sequence[:]
def testAccessByPosition(self):
ft = IndexedFastaReader(self.FASTAPATH)
r000001 = ft[0]
assert "<IndexedFastaRecord: ref000001|EGFR_Exon_2>" == repr(r000001)
firstTwo = ft[:2]
assert [ft[0], ft[1]] == firstTwo
lastTwo = ft[-2:]
assert [ft[-2], ft[-1]] == lastTwo
def testSlice(self):
ft = IndexedFastaReader(self.FASTAPATH)
r000021 = ft["ref000021|EGFR_Exon_22"]
sequence = r000021.sequence
assert "CACTGCCTCA" == sequence[0:10]
assert "GCCAAGCTGG" == sequence[-10:]
assert "G" == sequence[-1]
assert "T" == sequence[-3]
assert "C" == sequence[0]
assert "A" == sequence[1]
def test_dosLineEndingsFasta(self):
fr = FastaReader(data.getDosFormattedFasta())
frEntries = list(fr)
ft = IndexedFastaReader(data.getDosFormattedFasta())
ftEntries = list(ft)
assert len(frEntries) == len(ftEntries)
for (frE, ftE) in zip(frEntries, ftEntries):
assert frE.header == ftE.header
assert frE.sequence == ftE.sequence[:]
def test_readWeirdFastaIndex(self):
f = IndexedFastaReader(data.getWeird())
entries = list(f)
assert 1 == len(entries)
assert "chr1" == entries[0].header
assert "acgtacgtacgtact" == entries[0].sequence[:]
def _run_and_validate(args, file_name):
self._run_cmd_with_output(cmd, ofn)
aset = AlignmentSet(ofn, strict=True)
for res in aset.externalResources:
assert res.reference == otherdata.getFasta()
