mutalyzer-spdi-parser 0.2.0

Mutalyzer SPDI variant description parser.

Mutalyzer HGVS Parser

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---

Package to syntax check and convert SPDI descriptions into a dictionary model.

Quick start

Parse and convert a description from the command line:

.. code-block:: console

$ mutalyzer_spdi_parser -cs "NG_012337.3:10:C:T"
{
  "seq_id": "NG_012337.3",
  "position": 10,
  "deleted_sequence": "C",
  "inserted_sequence": "T"
}

$ mutalyzer_spdi_parser -ch "NG_012337.3:10:C:T"
{
  "type": "description_dna",
  "reference": {
    "id": "NG_012337.3"
  },
  "variants": [
    {
      "type": "deletion_insertion",
      "location": {
        "type": "range",
        "start": {
          "type": "point",
          "position": 10
        },
        "end": {
          "type": "point",
          "position": 11
        }
      },
      "deleted": [
        {
          "sequence": "C",
          "source": "description"
        }
      ],
      "inserted": [
        {
          "sequence": "T",
          "source": "description"
        }
      ]
    }
  ]
}

The to_hgvs_internal_model() function can be used to obtain the equivalent HGVS dictionary model (deletion insertion variants with internal locations and indexing):

.. code:: python

>>> from mutalyzer_spdi_parser import to_hgvs_internal_model
>>> model = to_hgvs_internal_model("NG_012337.3:10:C:T")
>>> model['reference']
{'id': 'NG_012337.3'}