INNER CODE UNIT · Python

unpadded_aa_position

sanger-pathogens/ariba · ariba/aln_to_metadata.py:222

                        unpadded_aa_position = unpadded_nt_position // 3

                        if unpadded_aa_sequences[seqname][unpadded_aa_position] in {variant.wild_value, variant.variant_value}:
                            variant_string = variant.wild_value
                        else:
                            variant_string = unpadded_aa_sequences[seqname][unpadded_aa_position]
                        variant_string += str(unpadded_aa_position + 1) + variant.variant_value
                    else:
                        if unpadded_sequences[seqname][unpadded_nt_position] in {variant.wild_value, variant.variant_value}:
                            variant_string = variant.wild_value
                        else:
                            variant_string = unpadded_sequences[seqname][unpadded_nt_position]
                        variant_string += str(unpadded_nt_position + 1) + variant.variant_value

                    lines.append('\t'.join([seqname, is_gene, is_var_only, variant_string, variant.identifier, description]))

        return lines

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