def test_next_with_GT(self):
"""Parse a file which already in Genotype format"""
vcf_filename = os.path.join(test_data(), 'file_with_SNPs_in_GT_format.aln.vcf')
vcf_file = open(vcf_filename, 'r')
reader = SNPSitesReader(vcf_file)
record = reader.next()
samples = record.samples
samples_with_alternative_bases = [sample.sample for sample in samples if
sample.data.GT != '0']
expected = ['3002_8_1', '3002_8_2', '3002_8_6', '4056_2_10', '4056_2_4',
'4056_8_6', '5174_5_1', '5174_5_7', '5174_5_9', '5174_6_10',
'5174_7_1', '5174_8_5']
self.assertItemsEqual(samples_with_alternative_bases, expected)
def test_next(self):
"""Parse a file with Alternate Base info
File was cerated using snp-sites"""
vcf_filename = os.path.join(test_data(), 'file_with_SNPs.aln.vcf')
vcf_file = open(vcf_filename, 'r')
reader = SNPSitesReader(vcf_file)
record = reader.next()
samples = record.samples
samples_with_alternative_bases = [sample.sample for sample in samples if
sample.data.GT != '0']
expected = ['3002_8_1', '3002_8_2', '3002_8_6', '4056_2_10', '4056_2_4',
'4056_8_6', '5174_5_1', '5174_5_7', '5174_5_9', '5174_6_10',
'5174_7_1', '5174_8_5']
self.assertItemsEqual(samples_with_alternative_bases, expected)
