mmtfPyspark.datasets.g2sDataset module¶

g2sDataset.py

This class maps human genetic variation positions to PDB structure positions. Genomic positions must be specified for the hgvs-grch37 reference genome using the HGVS sequence variant nomenclature.

References¶

HGVS sequence variant nomenclature http://varnomen.hgvs.org/
G2S Web Services https://g2s.genomenexus.org/
Juexin Wang, Robert Sheridan, S Onur Sumer, Nikolaus Schultz, Dong Xu, Jianjiong Gao; G2S: a web-service for annotating genomic variants on 3D protein structures (2018) Bioinformatics. https://doi.org/10.1093/bioinformatics/bty047

Examples¶

>>> variantIds = ["chr7:g.140449098T>C", "chr7:g.140449100T>C"]
>>> ds = g2sDataset.get_position_dataset(variantIds, "3TV4", "A")
>>> ds.show()
+-----------+-------+-----------+------------+-----------+-------------------+
|structureId|chainId|pdbPosition|pdbAminoAcid|  refGenome|        variationId|
+-----------+-------+-----------+------------+-----------+-------------------+
|       3TV4|      A|        661|           N|hgvs-grch37|chr7:g.140449098T>C|
|       3TV4|      A|        660|           N|hgvs-grch37|chr7:g.140449100T>C|
+-----------+-------+-----------+------------+-----------+-------------------+

get_full_dataset(variationIds, structureId=None, chainId=None)[source]¶

Downloads PDB residue mappings and alignment information for a list of genomic variations

Parameters:

Parameters:	variationIds : list genomic variation ids, e.g. chr7:g.140449103A>C structureId : str specific PDB structure used for mapping [None] chainId : str specific chain used for mapping [None]
Returns:	dataset dataset with PDB mapping information

variationIds : list

genomic variation ids, e.g. chr7:g.140449103A>C

structureId : str

specific PDB structure used for mapping [None]

chainId : str

specific chain used for mapping [None]

Returns:

dataset

dataset with PDB mapping information

get_position_dataset(variationIds, structureId=None, chainId=None)[source]¶

Downloads PDB residue mappings for a list of genomic variations