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import pysam
import pytest
from TestUtils import make_data_files, CBCF_DATADIR
def setUpModule():
make_data_files(CBCF_DATADIR)
@pytest.fixture
def vcf_header():
vcf_header = pysam.VariantHeader()
vcf_header.add_samples("sample1", "sample2")
vcf_header.contigs.add("1")
return vcf_header
## segfault without coordinates
def test_ascii_annotation_can_be_added(vcf_header):
vcf_header.formats.add("AN", 1, "String", "An annotation")
record = vcf_header.new_record(
contig="1",
start=12,
stop=13,
samples=[
{"AN": "anno1"},
{"AN": "anno2"}])
assert str(record)[:-1].split("\t")[-2:] == ["anno1", "anno2"]
def test_ascii_annotation_with_variable_length_can_be_added(vcf_header):
vcf_header.formats.add("AN", 1, "String", "An annotation")
record = vcf_header.new_record(
contig="1",
start=12,
stop=13,
samples=[
{"AN": "anno1b"},
{"AN": "anno1"}])
assert str(record)[:-1].split("\t")[-2:] == ["anno1b", "anno1"]
record = vcf_header.new_record(
contig="1",
start=12,
stop=13,
samples=[
{"AN": "anno2"},
{"AN": "anno2b"}])
assert str(record)[:-1].split("\t")[-2:] == ["anno2", "anno2b"]
def test_unicode_annotation_can_be_added(vcf_header):
vcf_header.formats.add("AN", 1, "String", "An annotation")
record = vcf_header.new_record(
contig="1",
start=12,
stop=13,
samples=[
{"AN": "anno1"},
{"AN": "Friedrich-Alexander-Universit\u00E4t_Erlangen-N\u00FCrnberg"}])
assert str(record)[:-1].split("\t")[-2:] == [
"anno1",
"Friedrich-Alexander-Universit\u00E4t_Erlangen-N\u00FCrnberg"]
def test_set_sample_alleles(vcf_header):
vcf_header.formats.add('GT',1,'String',"Genotype") # id, number, type, description
record = vcf_header.new_record(
contig="1",
start=20,
stop=21,
alleles=('A','T')
)
record.samples['sample1'].alleles = ('T', 'A')
assert record.samples['sample1'].alleles == ('T','A')
# Empty record:
record.samples['sample1'].alleles = (None, )
assert record.samples['sample1'].alleles == tuple()
record.samples['sample1'].alleles = None
assert record.samples['sample1'].alleles == tuple()
record.samples['sample1'].alleles = tuple()
assert record.samples['sample1'].alleles == tuple()
# check error conditions:
with pytest.raises(ValueError, match='One or more of the supplied sample alleles are not defined'):
record.samples['sample1'].alleles = ('C', 'A')
with pytest.raises(ValueError, match='Use .allele_indices to set integer allele indices'):
record.samples['sample1'].alleles = (1, 0)
def test_repeated_new_record(vcf_header):
vcf_header.formats.add('GT', 1, 'String', "Genotype")
vcf_header.formats.add("AA", 1, "String", "An annotation")
vcf_header.formats.add("BB", 1, "String", "Another annotation")
data = {'id': 'INS_1', 'contig': '1', 'start': 10, 'stop': 15, 'alleles': ['A', 'TCGA'],
'samples': [{'AA': ('one'), 'GT': (0, 1), 'BB': ('two')},
{'GT': (1, 0), 'BB': ('three')}]}
record1 = vcf_header.new_record(**data)
assert '\tGT:' in str(record1) # Verify that GT is output first
assert record1.samples['sample1'].alleles == ('A', 'TCGA')
assert record1.samples['sample2'].alleles == ('TCGA', 'A')
record2 = vcf_header.new_record(**data)
assert '\tGT:' in str(record2) # Verify that GT is actually emitted and is output first
assert record2.samples['sample1'].alleles == ('A', 'TCGA')
assert record2.samples['sample2'].alleles == ('TCGA', 'A')
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