def test_writer(yrb_writer, capsys):
yrb_writer = kevlar.vcf.VCFWriter(sys.stdout, source='py.test')
yrb_writer.register_sample('NA19238')
yrb_writer.register_sample('NA19239')
yrb_writer.register_sample('NA19240')
yrb_writer.describe_format('GT', 'String', '1', 'Genotype')
yrb_writer.write_header()
v = Variant('1', 12345, 'G', 'C')
v.annotate('PART', '42')
v.annotate('CONTIG', 'A' * 100)
v.format('NA19238', 'GT', '0/0')
v.format('NA19239', 'GT', '0/0')
v.format('NA19240', 'GT', '0/1')
v.format('NA19238', 'ALTABUND', '12,9,8')
v.format('NA19239', 'ALTABUND', '0,0,0')
v.format('NA19240', 'ALTABUND', '0,0,0')
yrb_writer.write(v)
out, err = capsys.readouterr()
print(out)
outlines = out.strip().split('\n')
fmtlines = [l for l in outlines if l.startswith('##FORMAT')]
assert len(fmtlines) == 2
gtfmt = '##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">'
assert gtfmt in fmtlines
varlines = [l for l in outlines if not l.startswith('#')]
assert len(varlines) == 1
values = varlines[0].split('\t')
assert len(values) == 12
assert values[8:12] == [
'ALTABUND:GT', '12,9,8:0/0', '0,0,0:0/0', '0,0,0:0/1'
]
def test_writer_bad_fmt(yrb_writer):
v = Variant('1', 12345, 'G', 'C')
v.annotate('PART', '42')
v.annotate('CONTIG', 'A' * 100)
v.format('NA19238', 'GT', '0/0')
v.format('NA19240', 'GT', '0/1')
v.format('NA19239', 'ALTABUND', '0,0,0')
v.format('NA19240', 'ALTABUND', '0,0,0')
errormsg = r'samples not annotated with the same FORMAT fields'
with pytest.raises(kevlar.vcf.VariantAnnotationError, match=errormsg):
yrb_writer.write(v)
def test_info():
"""Test handling of "info" field attributes.
This tests the mechanics of the .annotate() and .attribute() API, and the
FormattedList class underpinning it.
"""
values = FormattedList()
assert str(values) == '.'
values.append(42)
assert str(values) == '42'
values.append(1776)
assert str(values) == '42,1776'
values.append('B0gU$')
with pytest.raises(kevlar.vcf.KevlarMixedDataTypeError):
str(values)
v = Variant('1', 12345, 'G', 'C')
assert v.attribute('VW') is None
v.annotate('VW', 'AGTNNNNNNNNNNNNNNNNNNNNNTGA')
assert v.attribute('VW') == 'AGTNNNNNNNNNNNNNNNNNNNNNTGA'
v.annotate('VW', 'GATTACA')
assert v.attribute('VW') == 'GATTACA'
assert v.attribute('VW', pair=True) == 'VW=GATTACA'
v.annotate('VW', 'ATGCCCTAG', replace=False)
assert v.info['VW'] == ['GATTACA', 'ATGCCCTAG']
assert v.attribute('VW') == ['GATTACA', 'ATGCCCTAG']
assert v.attribute('VW', string=True) == 'GATTACA,ATGCCCTAG'
assert v.attribute('VW', pair=True) == 'VW=GATTACA,ATGCCCTAG'
v.annotate('VW', 'AAAAAAAAA', replace=False)
assert v.attribute('VW') == ['GATTACA', 'ATGCCCTAG', 'AAAAAAAAA']
assert v.attribute('VW', pair=True) == 'VW=GATTACA,ATGCCCTAG,AAAAAAAAA'
v.annotate('DROPPED', 3)
assert v.attribute('DROPPED') == 3
assert v.attribute('DROPPED', string=True) == '3'
v.annotate('DROPPED', 31, replace=False)
assert v.attribute('DROPPED') == [3, 31]
assert v.attribute('DROPPED', string=True) == '3,31'
assert v.attribute('DROPPED', pair=True) == 'DROPPED=3,31'
v.annotate('MATEDIST', 432.1234, replace=False)
v.annotate('MATEDIST', 8765.4321, replace=False)
assert v.attribute('MATEDIST', string=True) == '432.123,8765.432'
v.annotate('LLIH', -436.0111857750478)
assert v.attribute('LLIH', pair=True) == 'LLIH=-436.011'
