INNER CODE UNIT · Python

ref_unpadded_nt_position

sanger-pathogens/ariba · ariba/aln_to_metadata.py:202

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

                for seqname, seq in sorted(padded_sequences.items()):
                    if seqname == refname:
                        continue

                    if seq[padded_nt_position] == '-':
                        print('Warning: position has a gap in sequence ', seqname, 'corresponding to variant', variant, '(' + variant.identifier + ') in sequence ', refname, '... Ignoring for ' + seqname, file=sys.stderr)
                        continue

                    unpadded_nt_position = AlnToMetadata._padded_to_unpadded_nt_position(padded_nt_position, insertions[seqname])
                    assert unpadded_nt_position is not None

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