Library

The library provides a number of functions/classes to parse and convert descriptions.

The to_model() function

The to_model() function can be used to convert an HGVS description to a dictionary model.

>>> from mutalyzer_hgvs_parser import to_model
>>> model = to_model('NG_012337.1(SDHD_v001):c.274del')
>>> model['reference']
{'id': 'NG_012337.1', 'selector': {'id': 'SDHD_v001'}}

An alternative start rule can be used to parse a partial description. See Usage for the list of available start rules.

>>> from mutalyzer_hgvs_parser import to_model
>>> model = to_model('274del', 'variant')
>>> model
{'location': {'type': 'point', 'position': 274}, 'type': 'deletion', 'source': 'reference'}

The "source" field

The "source" field indicates where a sequence or location originates:

"description"

The sequence is written explicitly in the HGVS string.

>>> to_model('274G>T', 'variant')['deleted']
[{'sequence': 'G', 'source': 'description'}]

"reference"

The sequence or location is implied by HGVS convention; it must be retrieved from the (same) reference sequence.

>>> to_model('274del', 'variant')['source']
'reference'

>>> to_model('NG_012337.1:g.274_275ins100_200')['variants'][0]['inserted']
[{'location': {...}, 'source': 'reference'}]

{"id": "..."}

The sequence comes from an explicitly named external reference.

>>> to_model('NG_012337.1:g.274_275insNG_012337.3:g.100_200')['variants'][0]['inserted']
[{'type': 'description_dna', ..., 'source': {'id': 'NG_012337.3'}, ...}]

The parse() function

The parse() function checks whether a description is syntactically valid and raises an exception if not. Most users will want to_model() instead, which both checks validity and returns the dictionary model in one step. parse() is useful when you only need to validate and do not need the model, as it skips the conversion step.

>>> from mutalyzer_hgvs_parser import parse
>>> parse("LRG_1:100del")
Tree('description', ...)

The return value is a lark Tree object. Working with it directly requires familiarity with lark.

The HgvsParser class

For advanced use cases, such as supplying a custom grammar file or controlling whitespace handling, the HgvsParser class can be used directly. See the API documentation for details.