Package to syntax check and convert SPDI descriptions into a dictionary model.
Parse and convert a description from the command line:
$ 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):
>>> 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'}
