INNER CODE UNIT · Python

_check_variants_match_sequences

sanger-pathogens/ariba · ariba/aln_to_metadata.py:129

    def _check_variants_match_sequences(cls, unpadded_sequences, variants, seqs_are_coding, genetic_code=11):
        original_code = pyfastaq.sequences.genetic_code
        pyfastaq.sequences.genetic_code = genetic_code
        for seqname, variant_list in variants.items():
            if seqname not in unpadded_sequences:
                pyfastaq.sequences.genetic_code = original_code
                raise Error('Sequence name "' + seqname + '" given in variants file, but sequence not found')
            for variant, description in variant_list:
                if not variant.sanity_check_against_seq(unpadded_sequences[seqname], translate_seq=seqs_are_coding):
                    pyfastaq.sequences.genetic_code = original_code
                    raise Error('Variant "' + str(variant) + '" for sequence "' + seqname + '" does not match sequence. cannot continue')

        pyfastaq.sequences.genetic_code = original_code
        return True


    @classmethod
    def _variant_ids_are_unique(cls, variants):

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