mmtfPyspark.datasets.myVariantDataset module¶

References¶

• For more information: http://myvariant.info
• Query syntax: http://myvariant.info/docs/
• Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C (2016) High-performance web services for querying gene and variant annotation. Genome Biology 17(1):1-7. https://doi.org/10.1186/s13059-016-0953-9

Examples¶

Get all missense variations for a list of Uniprot Ids:

>>> uniprotIds = ['P15056']    # BRAF
>>> ds = MyVariantDataset.get_variations(uniprotIds)
>>> ds.show()

Return missense variations that match a query

>>> uniprotIds = ['P15056']    # BRAF
>>> query = "clinivar.rcv.clinical_significance:pathogenic"
...       + "OR linivar.rcv.clinical_significance:likely pathogenic"
>>> ds = MyVariantDataset.get_variations(uniprotIds, query)
>>> ds.show()
+-------------------+---------+
|        variationId|uniprotId|
+-------------------+---------+
|chr7:g.140454006G>T|   P15056|
|chr7:g.140453153A>T|   P15056|
|chr7:g.140477853C>A|   P15056|
+-------------------+---------+

get_variations(uniprotIds, query='')[source]¶

Returns a dataset of missense variabtions for a list of Uniprot Ids and a MyVariant.info query.

Parameters:	uniprotIds : list list of Uniprot Ids query : str MyVariant.info query string [‘’]
Returns:	dataset dataset with variation Ids and Uniprot Ids or null if no data are found

References

query syntax http://myvariant.info/docs/

Examples

>>> uniprotIds = ['P15056']    # BRAF
>>> query = "clinivar.rcv.clinical_significance:pathogenic"
...         + "OR linivar.rcv.clinical_significance:likely pathogenic"
>>> ds = MyVariantDataset.get_variations(uniprotIds, query)