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'}
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"keywords": "Mutalyzer, HGVS, SPDI, description, parser, genomic",
"author": "Mihai Lefter",
"author_email": "M.Lefter@lumc.nl",
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"description": "Mutalyzer HGVS Parser\n=====================\n\n.. image:: https://img.shields.io/github/last-commit/mutalyzer/spdi-parser.svg\n :target: https://github.com/mutalyzer/spdi-parser/graphs/commit-activity\n.. image:: https://readthedocs.org/projects/mutalyzer-spdi-parser/badge/?version=latest\n :target: https://mutalyzer-spdi-parser.readthedocs.io/en/latest\n.. image:: https://img.shields.io/github/release-date/mutalyzer/spdi-parser.svg\n :target: https://github.com/mutalyzer/spdi-parser/releases\n.. image:: https://img.shields.io/github/release/mutalyzer/spdi-parser.svg\n :target: https://github.com/mutalyzer/spdi-parser/releases\n.. image:: https://img.shields.io/pypi/v/mutalyzer-spdi-parser.svg\n :target: https://pypi.org/project/mutalyzer-spdi-parser/\n.. image:: https://img.shields.io/github/languages/code-size/mutalyzer/spdi-parser.svg\n :target: https://github.com/mutalyzer/spdi-parser\n.. image:: https://img.shields.io/github/languages/count/mutalyzer/spdi-parser.svg\n :target: https://github.com/mutalyzer/spdi-parser\n.. image:: https://img.shields.io/github/languages/top/mutalyzer/spdi-parser.svg\n :target: https://github.com/mutalyzer/spdi-parser\n.. image:: https://img.shields.io/github/license/mutalyzer/spdi-parser.svg\n :target: https://raw.githubusercontent.com/mutalyzer/spdi-parser/master/LICENSE.md\n\n----\n\nPackage to syntax check and convert SPDI descriptions into a dictionary model.\n\n\nQuick start\n-----------\n\nParse and convert a description from the command line:\n\n.. code-block:: console\n\n $ mutalyzer_spdi_parser -cs \"NG_012337.3:10:C:T\"\n {\n \"seq_id\": \"NG_012337.3\",\n \"position\": 10,\n \"deleted_sequence\": \"C\",\n \"inserted_sequence\": \"T\"\n }\n\n $ mutalyzer_spdi_parser -ch \"NG_012337.3:10:C:T\"\n {\n \"type\": \"description_dna\",\n \"reference\": {\n \"id\": \"NG_012337.3\"\n },\n \"variants\": [\n {\n \"type\": \"deletion_insertion\",\n \"location\": {\n \"type\": \"range\",\n \"start\": {\n \"type\": \"point\",\n \"position\": 10\n },\n \"end\": {\n \"type\": \"point\",\n \"position\": 11\n }\n },\n \"deleted\": [\n {\n \"sequence\": \"C\",\n \"source\": \"description\"\n }\n ],\n \"inserted\": [\n {\n \"sequence\": \"T\",\n \"source\": \"description\"\n }\n ]\n }\n ]\n }\n\n\nThe ``to_hgvs_internal_model()`` function can be used to obtain the equivalent\nHGVS dictionary model (deletion insertion variants with internal locations and\nindexing):\n\n.. code:: python\n\n >>> from mutalyzer_spdi_parser import to_hgvs_internal_model\n >>> model = to_hgvs_internal_model(\"NG_012337.3:10:C:T\")\n >>> model['reference']\n {'id': 'NG_012337.3'}\n",
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