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_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_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_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_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())
