INNER CODE UNIT · Python

__init__

sanger-pathogens/ariba · ariba/aln_to_metadata.py:9

    def __init__(self,
      aln_file,
      vars_file,
      refs_are_coding,
      refs_are_variant_only,
      genetic_code=11,
    ):
        self.padded_seqs = AlnToMetadata._load_aln_file(aln_file)
        self.refs_are_coding = refs_are_coding
        self.refs_are_variant_only = refs_are_variant_only
        self.variants = AlnToMetadata._load_vars_file(vars_file, self.refs_are_coding)
        self.genetic_code = genetic_code


    @classmethod
    def _load_aln_file(cls, aln_file):
        seqs = {}
        pyfastaq.tasks.file_to_dict(aln_file, seqs)

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