Usage

The mutate() function provides an interface to mutate a sequence according to a list of variants. A dictionary with the reference ids as keys and their sequences as values should be provided as input. The reference with the reference key is the one to be mutate according to the variants model list, the second input of the mutate() function.

from mutalyzer_mutator import mutate

sequences = {"reference": "AAGG", "OTHER_REF": "AATTAA"}

variants = [
    # 2_2delinsOTHER_REF:2_4
    {
        "type": "deletion_insertion",
        "source": "reference",
        "location": {
            "type": "range",
            "start": {"type": "point", "position": 2},
            "end": {"type": "point", "position": 2},
        },
        "inserted": [
            {"sequence": "CC", "source": "description"},
            {
                "source": {"id": "OTHER_REF"},
                "location": {
                    "type": "range",
                    "start": {"type": "point", "position": 2},
                    "end": {"type": "point", "position": 4},
                },
            },
        ],
    }
]

observed = mutate(sequences, variants)  # observed = 'AACCTTGG'