def test_add_tag_values_raisesNotImplementedError(self):
class FakeTag(common_tags.AbstractJacquardTag):
def __init__(self):
pass
tag = FakeTag()
self.assertRaises(NotImplementedError, tag.add_tag_values,
VcfRecord("1", "42", "A", "C"))
def test_empty_record(self):
sample_names = ["SampleA"]
base = VcfRecord.parse_record(
self.entab("chr2|1|ID|A|C|QUAL|FILTER|INFO|F|S\n"), sample_names)
empty_record = base.get_empty_record()
expected_record = VcfRecord(chrom="chr2", pos="1", ref="A", alt="C")
self.assertEquals(expected_record.text(), empty_record.text())
def test_asTextExpandsEmptyTrailingFormatField(self):
sampleA = OrderedDict([('a', '1'), ('b', '2')])
sampleB = OrderedDict([('a', '10')])
sample_tag_values = OrderedDict([("SampleA", sampleA),
("SampleB", sampleB)])
record = VcfRecord("CHROM", "POS", "REF", "ALT", "ID", "QUAL",
"FILTER", "INFO", sample_tag_values)
expected = self.entab(
"CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|a:b|1:2|10:.\n")
self.assertEquals(expected, record.text())
def test_asTextWhenEmptyFormatField(self):
sampleA = OrderedDict({})
sampleB = OrderedDict({})
sample_tag_values = OrderedDict({
"SampleA": sampleA,
"SampleB": sampleB
})
record = VcfRecord("CHROM", "POS", "REF", "ALT", "ID", "QUAL",
"FILTER", "INFO", sample_tag_values)
expected = self.entab("CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|.|.|.\n")
self.assertEquals(expected, record.text())
def test_sample_field_whenInconsistentTags(self):
# FYI this should never happen in the wild, but I wanted to test the exception formatting.
sampleA = OrderedDict([('a', '1'), ('b', '2')])
sampleB = OrderedDict([('a', '10')])
sample_tag_values = OrderedDict([("SampleA", sampleA),
("SampleB", sampleB)])
record = VcfRecord("CHROM", "POS", "REF", "ALT", "ID", "QUAL",
"FILTER", "INFO", sample_tag_values)
self.assertRaisesRegexp(
ValueError,
r'CHROM:POS:REF:ALT|sample format tags are not consistent: requested tags \[a\] but sample has has tags \[a=1, b=2\] leaving behind \[b\]',
record._sample_field, ['a'], 'SampleA')
def test_text(self):
sampleA = OrderedDict(
sorted({
"F1": "SA.1",
"F2": "SA.2",
"F3": "SA.3"
}.items()))
sampleB = OrderedDict(
sorted({
"F1": "SB.1",
"F2": "SB.2",
"F3": "SB.3"
}.items()))
sample_tag_values = OrderedDict(
sorted({
"SampleA": sampleA,
"SampleB": sampleB
}.items()))
record = VcfRecord("CHROM", "POS", "REF", "ALT", "ID", "QUAL",
"FILTER", "INFO", sample_tag_values)
expected = self.entab(
"CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|F1:F2:F3|SA.1:SA.2:SA.3|SB.1:SB.2:SB.3\n"
)
self.assertEquals(expected, record.text())
def test_add_or_replace_filter_filtersOnlyAppendsUnique(self):
record = VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="indelError")
record.add_or_replace_filter("JQ_EXCLUDE")
record.add_or_replace_filter("JQ_EXCLUDE")
self.assertEquals("indelError;JQ_EXCLUDE", record.filter)
def test_add_or_replace_filter_duplicateFilterNotAdded(self):
record = VcfRecord("chr1", "42", "XYZ", "C", vcf_filter="JQ_EXCLUDE")
record.add_or_replace_filter("JQ_EXCLUDE")
self.assertEquals("JQ_EXCLUDE", record.filter)
def test_add_or_replace_filter_filterReplacesEmptyFilter(self):
record = VcfRecord("chr1", "42", "X", "C", vcf_filter="")
record.add_or_replace_filter("JQ_EXCLUDE")
self.assertEquals("JQ_EXCLUDE", record.filter)
def test_join_info_fields_orderedCorrectly(self):
vcf_record = VcfRecord("chr1", "2", "A", "G", info="FOO;BAR;BAZ")
vcf_record._join_info_fields()
self.assertEquals("FOO;BAR;BAZ", vcf_record.info)
def test_get_info_dict_null(self):
vcf_record = VcfRecord("chr1", "42", "A", "C", info=".")
self.assertEquals({}, vcf_record.info_dict)
