INNER CODE UNIT · Python

_make_unpadded_seqs

sanger-pathogens/ariba · ariba/aln_to_metadata.py:54

    def _make_unpadded_seqs(cls, padded_seqs):
        unpadded_seqs = {}
        for seq in padded_seqs.values():
            unpadded_seqs[seq.id] = pyfastaq.sequences.Fasta(seq.id, seq.seq.replace('-', ''))
        return unpadded_seqs


    @classmethod
    def _check_seq_lengths_same(cls, seqs):
        sequence_lengths = set([len(x) for x in seqs.values()])
        if len(sequence_lengths) > 1:
            raise Error('Input sequences must all be the same length. Cannot continue. Lengths found: ' + ','.join([str(x) for x in sequence_lengths]))
        return len(sequence_lengths) == 1


    @classmethod
    def _insertion_coords(cls, sequence):
        insertions = []

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