def test_sample_vcfs_return_infinite_positions(self):
vcf = Vcf(testdata.GATK_VCF, 'test_name', 'test_aliner', 'test_snpcaller')
contig = vcf.get_contig('500WT1_test')
positions = contig.positions
expected = (
Position(call='C', simple_call='C', coverage=19049, proportion='-'),
Position(call='C', simple_call='C', coverage=19049, proportion='-'),
Position(call='T', simple_call='T', coverage=18824, proportion='-'),
Position(call='G', simple_call='G', coverage=18804, proportion='-'),
Position(call='X', simple_call='N', coverage='?', proportion='?'),
Position(call='X', simple_call='N', coverage='?', proportion='?'),
Position(call='G', simple_call='G', coverage=18895, proportion='-'),
Position(call='A', simple_call='A', coverage=19005, proportion='-'),
)
# It should yield all the contig positions.
position = 0
for expect, observe in zip(expected, positions):
position += 1
self.assertEqual(expect, observe)
self.assertEqual(len(expected), position)
# It should yield empty positions after the contig is exhausted.
self.assertEqual(VcfContig.VCF_EMPTY_POSITION, next(positions))
self.assertEqual(VcfContig.VCF_EMPTY_POSITION, next(positions))
def test_sample_vcfs_return_infinite_positions(self):
vcf = Vcf(testdata.GATK_VCF, 'test_name', 'test_aliner',
'test_snpcaller')
contig = vcf.get_contig('500WT1_test')
positions = contig.positions
expected = (
Position(call='C', simple_call='C', coverage=19049,
proportion='-'),
Position(call='C', simple_call='C', coverage=19049,
proportion='-'),
Position(call='T', simple_call='T', coverage=18824,
proportion='-'),
Position(call='G', simple_call='G', coverage=18804,
proportion='-'),
Position(call='X', simple_call='N', coverage='?', proportion='?'),
Position(call='X', simple_call='N', coverage='?', proportion='?'),
Position(call='G', simple_call='G', coverage=18895,
proportion='-'),
Position(call='A', simple_call='A', coverage=19005,
proportion='-'),
)
# It should yield all the contig positions.
position = 0
for expect, observe in zip(expected, positions):
position += 1
self.assertEqual(expect, observe)
self.assertEqual(len(expected), position)
# It should yield empty positions after the contig is exhausted.
self.assertEqual(VcfContig.VCF_EMPTY_POSITION, next(positions))
self.assertEqual(VcfContig.VCF_EMPTY_POSITION, next(positions))
def test_varscan_call_cannot_be_made(self):
"""
VarScan may include a position with ALT values when a call cannot be made.
It should still be called missing (X).
TODO: Add See Also VarScan documentation
"""
# The following is from a SRR011186 sample using bwamem and varscan.
# The positions from the source data were 34072-34074.
vcf_data = (
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR011186\n"
"gi|561108321|ref|NC_018143.2| 1 . GC C . PASS ADP=114;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:114:114:6:108:94.74%:1.6043E-58:40:38:2:4:46:62\n"
# This position should be called missing because the GT column is './.'
"gi|561108321|ref|NC_018143.2| 2 . C G . PASS ADP=108;WT=1;HET=0;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR ./.:.:108\n"
"gi|561108321|ref|NC_018143.2| 3 . A . . PASS ADP=112;WT=1;HET=0;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/0:209:112:112:111:0:0%:1E0:38:0:47:64:0:0\n"
)
expected = (Position(call='G',
simple_call='G',
coverage=114,
proportion=0.05263157894736842),
Position(call='X',
simple_call='N',
coverage=108.0,
proportion='-'),
Position(call='A',
simple_call='A',
coverage=112,
proportion=0.9910714285714286))
with tempfile.NamedTemporaryFile('w+') as tmpfile:
# Seed the file with test data
tmpfile.write(vcf_data)
tmpfile.seek(0)
# Find the test contig.
vcf = Vcf(tmpfile.name, 'SRR011186', 'varscan', 'bwamem')
contig = vcf.get_contig('gi|561108321|ref|NC_018143.2|')
positions = contig.positions
self.assertIsInstance(contig, VcfContig)
# Check position values.
position = 0
for expect, observe in zip(expected, positions):
position += 1
self.assertEqual(expect, observe)
# It yields all expected positions
self.assertEqual(position, len(expected))
# All following positions should be empty
self.assertEqual(VcfContig.VCF_EMPTY_POSITION, next(positions))
def test_varscan_call_cannot_be_made(self):
"""
VarScan may include a position with ALT values when a call cannot be made.
It should still be called missing (X).
TODO: Add See Also VarScan documentation
"""
# The following is from a SRR011186 sample using bwamem and varscan.
# The positions from the source data were 34072-34074.
vcf_data = (
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR011186\n"
"gi|561108321|ref|NC_018143.2| 1 . GC C . PASS ADP=114;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:114:114:6:108:94.74%:1.6043E-58:40:38:2:4:46:62\n"
# This position should be called missing because the GT column is './.'
"gi|561108321|ref|NC_018143.2| 2 . C G . PASS ADP=108;WT=1;HET=0;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR ./.:.:108\n"
"gi|561108321|ref|NC_018143.2| 3 . A . . PASS ADP=112;WT=1;HET=0;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/0:209:112:112:111:0:0%:1E0:38:0:47:64:0:0\n"
)
expected = (
Position(call='G', simple_call='G', coverage=114, proportion=0.05263157894736842),
Position(call='X', simple_call='N', coverage=108.0, proportion='-'),
Position(call='A', simple_call='A', coverage=112, proportion=0.9910714285714286)
)
with tempfile.NamedTemporaryFile('w+') as tmpfile:
# Seed the file with test data
tmpfile.write(vcf_data)
tmpfile.seek(0)
# Find the test contig.
vcf = Vcf(tmpfile.name, 'SRR011186', 'varscan', 'bwamem')
contig = vcf.get_contig('gi|561108321|ref|NC_018143.2|')
positions = contig.positions
self.assertIsInstance(contig, VcfContig)
# Check position values.
position = 0
for expect, observe in zip(expected, positions):
position += 1
self.assertEqual(expect, observe)
# It yields all expected positions
self.assertEqual(position, len(expected))
# All following positions should be empty
self.assertEqual(VcfContig.VCF_EMPTY_POSITION, next(positions))
def setUp(self):
self.vcf = Vcf(testdata.GATK_VCF, 'test_vcf', 'test_aligner', 'test_snpcaller')
class VcfTestCase(unittest.TestCase):
@classmethod
def setUp(self):
self.vcf = Vcf(testdata.GATK_VCF, 'test_vcf', 'test_aligner', 'test_snpcaller')
def test_repr(self):
expected = "Vcf(filepath='{0}', name='test_vcf', aligner='test_aligner', snpcaller='test_snpcaller')".format(
testdata.GATK_VCF)
self.assertEqual(expected, repr(self.vcf))
def test_identifier(self):
expected = 'test_vcf::test_aligner,test_snpcaller'
self.assertEqual(expected, self.vcf.identifier)
def test_get_contig(self):
"""
The following tests assume VcfContig is working.
"""
# It should return the correct contig at any file position or in any order.
contigs = (
'500WT1_test',
)
for contig_name in contigs:
contig = self.vcf.get_contig('500WT1_test')
# Ensure it is not an EmptyContig
self.assertIsInstance(contig, VcfContig)
self.assertEqual(contig_name, contig.name)
def test_get_contig_empty(self):
# If the sample does not contain a contig, it should return an EmptyContig placeholder.
contig = self.vcf.get_contig('DoesNotExist')
self.assertIsInstance(contig, EmptyContig)
def test_varscan_call_cannot_be_made(self):
"""
VarScan may include a position with ALT values when a call cannot be made.
It should still be called missing (X).
TODO: Add See Also VarScan documentation
"""
# The following is from a SRR011186 sample using bwamem and varscan.
# The positions from the source data were 34072-34074.
vcf_data = (
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR011186\n"
"gi|561108321|ref|NC_018143.2| 1 . GC C . PASS ADP=114;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:114:114:6:108:94.74%:1.6043E-58:40:38:2:4:46:62\n"
# This position should be called missing because the GT column is './.'
"gi|561108321|ref|NC_018143.2| 2 . C G . PASS ADP=108;WT=1;HET=0;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR ./.:.:108\n"
"gi|561108321|ref|NC_018143.2| 3 . A . . PASS ADP=112;WT=1;HET=0;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/0:209:112:112:111:0:0%:1E0:38:0:47:64:0:0\n"
)
expected = (
Position(call='G', simple_call='G', coverage=114, proportion=0.05263157894736842),
Position(call='X', simple_call='N', coverage=108.0, proportion='-'),
Position(call='A', simple_call='A', coverage=112, proportion=0.9910714285714286)
)
with tempfile.NamedTemporaryFile('w+') as tmpfile:
# Seed the file with test data
tmpfile.write(vcf_data)
tmpfile.seek(0)
# Find the test contig.
vcf = Vcf(tmpfile.name, 'SRR011186', 'varscan', 'bwamem')
contig = vcf.get_contig('gi|561108321|ref|NC_018143.2|')
positions = contig.positions
self.assertIsInstance(contig, VcfContig)
# Check position values.
position = 0
for expect, observe in zip(expected, positions):
position += 1
self.assertEqual(expect, observe)
# It yields all expected positions
self.assertEqual(position, len(expected))
# All following positions should be empty
self.assertEqual(VcfContig.VCF_EMPTY_POSITION, next(positions))
def setUp(self):
self.vcf = Vcf(testdata.GATK_VCF, 'test_vcf', 'test_aligner',
'test_snpcaller')
class VcfTestCase(unittest.TestCase):
@classmethod
def setUp(self):
self.vcf = Vcf(testdata.GATK_VCF, 'test_vcf', 'test_aligner',
'test_snpcaller')
def test_repr(self):
expected = "Vcf(filepath='{0}', name='test_vcf', aligner='test_aligner', snpcaller='test_snpcaller')".format(
testdata.GATK_VCF)
self.assertEqual(expected, repr(self.vcf))
def test_identifier(self):
expected = 'test_vcf::test_aligner,test_snpcaller'
self.assertEqual(expected, self.vcf.identifier)
def test_get_contig(self):
"""
The following tests assume VcfContig is working.
"""
# It should return the correct contig at any file position or in any order.
contigs = ('500WT1_test', )
for contig_name in contigs:
contig = self.vcf.get_contig('500WT1_test')
# Ensure it is not an EmptyContig
self.assertIsInstance(contig, VcfContig)
self.assertEqual(contig_name, contig.name)
def test_get_contig_empty(self):
# If the sample does not contain a contig, it should return an EmptyContig placeholder.
contig = self.vcf.get_contig('DoesNotExist')
self.assertIsInstance(contig, EmptyContig)
def test_varscan_call_cannot_be_made(self):
"""
VarScan may include a position with ALT values when a call cannot be made.
It should still be called missing (X).
TODO: Add See Also VarScan documentation
"""
# The following is from a SRR011186 sample using bwamem and varscan.
# The positions from the source data were 34072-34074.
vcf_data = (
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR011186\n"
"gi|561108321|ref|NC_018143.2| 1 . GC C . PASS ADP=114;WT=0;HET=0;HOM=1;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 1/1:255:114:114:6:108:94.74%:1.6043E-58:40:38:2:4:46:62\n"
# This position should be called missing because the GT column is './.'
"gi|561108321|ref|NC_018143.2| 2 . C G . PASS ADP=108;WT=1;HET=0;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR ./.:.:108\n"
"gi|561108321|ref|NC_018143.2| 3 . A . . PASS ADP=112;WT=1;HET=0;HOM=0;NC=0 GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR 0/0:209:112:112:111:0:0%:1E0:38:0:47:64:0:0\n"
)
expected = (Position(call='G',
simple_call='G',
coverage=114,
proportion=0.05263157894736842),
Position(call='X',
simple_call='N',
coverage=108.0,
proportion='-'),
Position(call='A',
simple_call='A',
coverage=112,
proportion=0.9910714285714286))
with tempfile.NamedTemporaryFile('w+') as tmpfile:
# Seed the file with test data
tmpfile.write(vcf_data)
tmpfile.seek(0)
# Find the test contig.
vcf = Vcf(tmpfile.name, 'SRR011186', 'varscan', 'bwamem')
contig = vcf.get_contig('gi|561108321|ref|NC_018143.2|')
positions = contig.positions
self.assertIsInstance(contig, VcfContig)
# Check position values.
position = 0
for expect, observe in zip(expected, positions):
position += 1
self.assertEqual(expect, observe)
# It yields all expected positions
self.assertEqual(position, len(expected))
# All following positions should be empty
self.assertEqual(VcfContig.VCF_EMPTY_POSITION, next(positions))