INNER CODE UNIT · Python

_insertion_coords

sanger-pathogens/ariba · ariba/aln_to_metadata.py:70

    def _insertion_coords(cls, sequence):
        insertions = []
        regex = re.compile('-+')
        for m in regex.finditer(sequence.seq):
             insertions.append(pyfastaq.intervals.Interval(m.span()[0], m.span()[1] - 1))
        return insertions


    @classmethod
    def _make_unpadded_insertion_coords(cls, unpadded_sequences):
        return {x.id: AlnToMetadata._insertion_coords(x) for x in unpadded_sequences.values()}


    @classmethod
    def _check_insertion_coords(cls, sequence):
        insertions = AlnToMetadata._insertion_coords(sequence)
        for coords in insertions:
            if coords.start % 3 !=0:

View source record →