INNER CODE UNIT · Python

_check_sequences

sanger-pathogens/ariba · ariba/aln_to_metadata.py:117

    def _check_sequences(cls, padded_sequences, unpadded_sequences, seqs_are_coding, genetic_code=11):
        AlnToMetadata._check_seq_lengths_same(padded_sequences)

        if seqs_are_coding:
            for sequence in unpadded_sequences.values():
                AlnToMetadata._check_insertion_coords(sequence)
                AlnToMetadata._check_coding_seq(sequence, genetic_code=genetic_code)

        return True


    @classmethod
    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

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