ensembl.Ensembl

Description:
Client for the Ensembl REST API. Supports gene, variant, phenotype, sequence, mapping, and overlap queries. There are a lot of different functionalities in each of the different methods so please test different options to see which one is best suited for your needs.

Variation methods

from benchmate.apis.ensembl import Ensembl
from benchmate.ranges.genomicranges import GenomicRange

ensembl = Ensembl()

# Variation info
info = ensembl.variation("rs56116432", add_annotations=True) # if you do not use the add annotations option the response would be a lot smaller

# this returns all the variants that are mentioned in a specific paper keep in mind that if you are looking for a very recent
# paper it might not be available yet
info_pub = ensembl.variation("26318936", method="publication", pubtype="pubmed")

# translate method translates one variant representation to other formats
info_translated = ensembl.variation("rs56116432", method="translate")
info_translated.results

VEP

VEP is Ensembl’s Variant Effect Predictor. You can run VEP on a single variant and return a lot of information based on what additionaly tools you have selected to use. To be able to use the VEP method you will need to use ccm_benchmate.variant.variant module.

from benchmate.variant.variant import SequenceVariant
myvar= SequenceVariant(1, 55051215, 'G', 'GA')

vep_info = ensembl.vep(species="human", variant=myvar, tools=None)
vep_info.results

There are many tools that can be called with the VEP method. You can see the whole list in the VEP website

Phenotype

If you are interested in what phenotypes are associated with a genomic region you can use the GenomicRanges module and the phenotype method:

from benchmate.ranges.genomicranges import GenomicRange
grange = GenomicRange(9, 22125503, 22125520, "+")
phenotypes = ensembl.phenotype(grange)
phenotypes

# or for a given range you can search for overlapping features (you can also do this in the genome module and it's the preffered method if you are planning to query a lot of different things)
overlap = ensembl.overlap(grange, features=["transcript"])

Mapping

If you have some genomic feature id and you want to convert them to something else you can use the mapping method. This could mean convering genomic coordinates to cDNA or protein coordinates to genomic coordinates etc.

ensembl.mapping("ENST00000650946", 100, 120, type="cDNA")

xrefs

Ensembl is a massive resource, it contains constantly updated cross-references to other databases. This is especially useful in our case because we can use this method to retrieve ids which then can be used to query other enpoints.

xrefs = ensembl.xrefs("ENSG00000139618")

Finally, you can return about the species, and the kinds of information that is available in the api (there may be changes and that is beyond our control) using Ensembl.info method.