solvebio/contrib/vcf_parser/vcf_parser.py
def row_to_dict(self, row, allele, alternate_alleles):
        """Return a parsed dictionary for JSON."""

        def _variant_sbid(**kwargs):
            """Generates a SolveBio variant ID (SBID)."""
            return '{build}-{chromosome}-{start}-{stop}-{allele}'\
                .format(**kwargs).upper()

        if allele == '.':
            # Try to use the ref, if '.' is supplied for alt.
            allele = row.REF or allele

        genomic_coordinates = {
            'build': self.genome_build,
            'chromosome': row.CHROM,
            'start': row.POS,
            'stop': row.POS + len(row.REF) - 1
        }

        # SolveBio standard variant format
        variant_sbid = _variant_sbid(allele=allele,
                                     **genomic_coordinates)

        return {
            'genomic_coordinates': genomic_coordinates,
            'variant': variant_sbid,
            'allele': allele,
            'row_id': row.ID,
            'reference_allele': row.REF,
            'alternate_alleles': alternate_alleles,
            'info': self._parse_info(row.INFO),
            'qual': row.QUAL,
            'filter': row.FILTER
        }
def row_to_dict(self, row, allele, alternate_alleles):
        """Return a parsed dictionary for JSON."""

        def _variant_sbid(**kwargs):
            """Generates a SolveBio variant ID (SBID)."""
            return '{build}-{chromosome}-{start}-{stop}-{allele}'\
                .format(**kwargs).upper()

        if allele == '.':
            # Try to use the ref, if '.' is supplied for alt.
            allele = row.REF or allele

        genomic_coordinates = {
            'build': self.genome_build,
            'chromosome': row.CHROM,
            'start': row.POS,
            'stop': row.POS + len(row.REF) - 1
        }

        # SolveBio standard variant format
        variant_sbid = _variant_sbid(allele=allele,
                                     **genomic_coordinates)

        return {
            'genomic_coordinates': genomic_coordinates,
            'variant': variant_sbid,
            'allele': allele,
            'row_id': row.ID,
            'reference_allele': row.REF,
            'alternate_alleles': alternate_alleles,
            'info': self._parse_info(row.INFO),
            'qual': row.QUAL,
            'filter': row.FILTER
        }
Return a parsed dictionary for JSON.