INNER CODE UNIT · Python

_check_insertion_coords

sanger-pathogens/ariba · ariba/aln_to_metadata.py:84

    def _check_insertion_coords(cls, sequence):
        insertions = AlnToMetadata._insertion_coords(sequence)
        for coords in insertions:
            if coords.start % 3 !=0:
                raise Error('Insertion does not start in frame in sequence "' + sequence.id + '". Cannot continue')
            elif len(coords) % 3 != 0:
                raise Error('Insertion of length not a mulitple of 3 in sequence "' + sequence.id + '". Cannot continue')

        return True


    @classmethod
    def _check_coding_seq(cls, sequence, genetic_code=11):
        if len(sequence) % 3 != 0:
            raise Error('Length of sequence ' + sequence.id + ' is ' + str(len(sequence)) + ', which is not a multiple of 3. Cannot continue')

        original_code = pyfastaq.sequences.genetic_code
        pyfastaq.sequences.genetic_code = genetic_code

View source record →