Usage

This package provides a command line interface.

Syntax check

To only check if a description can be successfully parsed.

$ mutalyzer_hgvs_parser 'NG_012337.1(SDHD_v001):c.274G>T'
Successfully parsed:
 NG_012337.1(SDHD_v001):c.274G>T

Description model

To obtain the model of a description add the -c flag.

$ mutalyzer_hgvs_parser -c 'NG_012337.1(SDHD_v001):c.274G>T'
{
  "reference": {
    "id": "NG_012337.1",
    "selector": {
      "id": "SDHD_v001"
    }
  },
  "coordinate_system": "c",
  "variants": [
    {
      "type": "substitution",
      "source": "reference",
      "location": {
        "type": "point",
        "position": 274
      },
      "deleted": [
        {
          "source": "description",
          "sequence": "G"
        }
      ],
      "inserted": [
        {
          "source": "description",
          "sequence": "T"
        }
      ]
    }
  ]
}

Grammar start rule

By default, the Mutalyzer grammar is used, with description as the start (top) rule. It is however possible to choose a different start rule with the -r option.

$ mutalyzer_hgvs_parser -r variant '274G>T'
Successfully parsed:
 274G>T

The -c flag can be employed together with a different start rule.

$ mutalyzer_hgvs_parser -c -r variant '274G>T'
{
  "location": {
    "type": "point",
    "position": 274
  },
  "type": "substitution",
  "source": "reference",
  "deleted": [
    {
      "sequence": "G",
      "source": "description"
    }
  ],
  "inserted": [
    {
      "sequence": "T",
      "source": "description"
    }
  ]
}

Parse tree representation

If pydot is installed, an image of the lark parse tree can be obtained with the -i option.

$ mutalyzer_hgvs_parser "274del" -r variant -i tree.png
Successfully parsed:
 274del
Parse tree image saved to:
 tree.png