INNER CODE UNIT · Python

_load_vars_file

sanger-pathogens/ariba · ariba/aln_to_metadata.py:31

    def _load_vars_file(cls, vars_file, refs_are_coding):
        var_type = 'p' if refs_are_coding else 'n'
        f = pyfastaq.utils.open_file_read(vars_file)
        variants = {}

        for line in f:
            try:
                ref_name, variant, identifier, description = line.rstrip().split('\t')
                variant = sequence_variant.Variant(var_type, variant, identifier)
            except:
                pyfastaq.utils.close(f)
                raise Error('Error in this line of variants file:\n' + line)

            if ref_name not in variants:
                variants[ref_name] = []

            variants[ref_name].append((variant, description))

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