Ensembl

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 import Ensembl
from benchmate.ranges 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 import SequenceVariant
myvar = SequenceVariant(chrom="1", pos=55051215, ref="G", alt="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 view all available VEP tools via:

ensembl.show_vep_tools()

Sequence & Homology

You can retrieve genomic, cDNA, or protein sequences directly by ID, or query orthologues and paralogues:

# Fetch sequence by accession or gene symbol
seq_data = ensembl.sequence(id="ENSG00000139618", sequence_type="genomic")

# Find orthologues for a gene in a target species
orthologues = ensembl.homology(id="ENSG00000139618", type="orthologues", target_species="mouse")

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

# Search for overlapping features (transcripts, exons, regulatory elements)
overlap = ensembl.overlap(grange, features=["transcript"])

Mapping

If you have a genomic feature ID and you want to convert coordinates to cDNA or protein positions (or vice versa), use the mapping method:

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

Xrefs & Info

Ensembl is a massive resource containing cross-references to other databases (UniProt, RefSeq, HGNC, etc.). Use xrefs to resolve IDs across platforms:

xrefs = ensembl.xrefs("ENSG00000139618")

Finally, you can inspect species list and available API features using ensembl.info().