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"
        }
      ]
    }
  ]
}

Parsing a partial description

By default the parser expects a complete HGVS description (e.g. NG_012337.1:g.274G>T). If you only have a part of a description — a bare variant, a location, or a reference — you can tell the parser where to start by passing a start rule with the -r option.

A start rule is the name of the grammar rule that the input must match. The most useful alternatives to the default (description) are:

Start rule	Matches
description	A complete HGVS description (default)
variant	A single variant without a reference, e.g. 274G>T or 10del
variants	A semicolon-separated list of variants, e.g. [274G>T;280del]
location	A position or range, e.g. 274 or 10_20
reference	A reference identifier, e.g. NG_012337.1 or NG_012337.1(SDHD_v001)
inserted	An inserted sequence, e.g. ATG or NG_012337.1:c.1_10

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

The -c flag can be combined with -r to convert a partial description to its model.

$ 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

An image of the parse tree can be obtained with the -i option. This requires Graphviz to be installed on your system (e.g. apt install graphviz on Debian/Ubuntu) and pydot:

pip install mutalyzer-hgvs-parser[plot]

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