INNER CODE UNIT · Python

_variants_to_tsv_lines

sanger-pathogens/ariba · ariba/aln_to_metadata.py:189

    def _variants_to_tsv_lines(cls, variants, unpadded_sequences, padded_sequences, insertions, seqs_are_coding, seqs_are_var_only):
        if seqs_are_coding:
            unpadded_aa_sequences = {x: unpadded_sequences[x].translate() for x in unpadded_sequences}
            is_gene = '1'
        else:
            is_gene = '0'

        is_var_only = '1' if seqs_are_var_only else '0'

        lines = []
        for refname in sorted(variants):
            for variant, description in variants[refname]:
                if seqs_are_coding:
                    ref_unpadded_nt_position = 3 * variant.position
                else:
                    ref_unpadded_nt_position = variant.position

                padded_nt_position = AlnToMetadata._unpadded_to_padded_nt_position(ref_unpadded_nt_position, insertions[refname])

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