Mutalyzer HGVS Parser

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Package to syntax check and convert Mutalyzer HGVS variant descriptions into a dictionary model to easily access descriptions information in a programmatically manner.

Features:

• Accepts HGVS descriptions with multiple variants (one HGVS allele).
• Any description sub-part can be parsed and converted as well.
• Supports common deviations to the HGVS guidelines.
• Command line and library interfaces available.

Quick start

Parse and convert a description from the command line:

$ mutalyzer_hgvs_parser -c "NG_012337.1:c.20del"
{
  "reference": {
    "id": "NG_012337.1"
  },
  "coordinate_system": "c",
  "variants": [
    {
      "location": {
        "type": "point",
        "position": 20
      },
      "type": "deletion",
      "source": "reference"
    }
  ]
}

The to_model() function can be used for the same purpose:

>>> from mutalyzer_hgvs_parser import to_model
>>> model = to_model("NG_012337.1:c.20del")
>>> model['reference']
{'id': 'NG_012337.1'}

Please see ReadTheDocs for the latest documentation.

Contents:

• Installation
  • From source
• Usage
  • Syntax check
  • Description model
  • Grammar start rule
  • Parse tree representation
• Command Line Interface
  • Positional Arguments
  • Named Arguments
• Grammar
• Library
  • The to_model() function
  • The parse() function
• API documentation
  • Hgvs parser
  • Convert
• Contributors