def genotypes(self): """ Extracts the genotypes from a VCF record """ alleles = vcf_allele_parser(self.data, self.field_format) return alleles
def test_vcf_allele_parser(): format = 'GT:DP:SOMETHING:SOMETHINGELSE' a = "0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,." expected = list(reversed([(2,1), (4,1), (5, 1)])) # stacks are FILO observed = vcf_allele_parser(a, format) assert observed.tolist() == expected
def test_vcf_allele_parser(): format = 'GT:DP:SOMETHING:SOMETHINGELSE' a = "0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,." expected = list(reversed([(2, 1), (4, 1), (5, 1)])) # stacks are FILO observed = vcf_allele_parser(a, format) assert observed.tolist() == expected
def genotypes(self): ''' Extract the genotypes from a VCF record ''' alleles = vcf_allele_parser(self.data, self.format) return alleles