def test_vcf_records_raisesStopIterationWhenExhausted(self):
file_contents = [
"##metaheader1\n",
self.entab("#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|SampleNormal|SampleTumor\n"),
self.entab("chr1|1|.|A|C|.|.|INFO|FORMAT|NORMAL|TUMOR\n"),
]
mock_reader = MockFileReader("my_dir/my_file.txt", file_contents)
reader = VcfReader(mock_reader)
reader.open()
record_iter = reader.vcf_records()
next(record_iter)
self.assertRaises(StopIteration, next, record_iter)
def test_vcf_records_raisesStopIterationWhenExhausted(self):
file_contents = [
"##metaheader1\n",
self.entab(
"#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|SampleNormal|SampleTumor\n"
),
self.entab("chr1|1|.|A|C|.|.|INFO|FORMAT|NORMAL|TUMOR\n")
]
mock_reader = MockFileReader("my_dir/my_file.txt", file_contents)
reader = VcfReader(mock_reader)
reader.open()
record_iter = reader.vcf_records()
next(record_iter)
self.assertRaises(StopIteration, next, record_iter)
def test_vcf_records(self):
file_contents = [
"##metaheader1\n",
"##metaheader2\n",
self.entab("#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|SampleNormal|SampleTumor\n"),
self.entab("chr1|1|.|A|C|.|.|INFO|FORMAT|NORMAL|TUMOR\n"),
self.entab("chr2|1|.|A|C|.|.|INFO|FORMAT|NORMAL|TUMOR"),
]
mock_reader = MockFileReader("my_dir/my_file.txt", file_contents)
reader = VcfReader(mock_reader)
actual_vcf_records = []
reader.open()
for vcf_record in reader.vcf_records():
actual_vcf_records.append(vcf_record)
reader.close()
self.assertEquals(2, len(actual_vcf_records))
self.assertEquals("chr1", actual_vcf_records[0].chrom)
self.assertEquals("chr2", actual_vcf_records[1].chrom)
self.assertTrue(mock_reader.open_was_called)
self.assertTrue(mock_reader.close_was_called)
def test_vcf_records(self):
file_contents = [
"##metaheader1\n", "##metaheader2\n",
self.entab(
"#CHROM|POS|ID|REF|ALT|QUAL|FILTER|INFO|FORMAT|SampleNormal|SampleTumor\n"
),
self.entab("chr1|1|.|A|C|.|.|INFO|FORMAT|NORMAL|TUMOR\n"),
self.entab("chr2|1|.|A|C|.|.|INFO|FORMAT|NORMAL|TUMOR")
]
mock_reader = MockFileReader("my_dir/my_file.txt", file_contents)
reader = VcfReader(mock_reader)
actual_vcf_records = []
reader.open()
for vcf_record in reader.vcf_records():
actual_vcf_records.append(vcf_record)
reader.close()
self.assertEquals(2, len(actual_vcf_records))
self.assertEquals('chr1', actual_vcf_records[0].chrom)
self.assertEquals('chr2', actual_vcf_records[1].chrom)
self.assertTrue(mock_reader.open_was_called)
self.assertTrue(mock_reader.close_was_called)