pyEnsemblRest

pyEnsemblRest is a simple Python client for the Ensembl REST API

License

pyEnsemblRest - A client for the Ensembl REST API written in the Python programming language

Copyright (C) 2013-2024, Steve Moss

pyEnsemblRest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

pyEnsemblRest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with pyEnsemblRest. If not, see <http://www.gnu.org/licenses/>.

Installation

Using pip

Simply type:

pip install pyensemblrest

From source

Clone the pyEnsemblRest repository then install the package from source:

git clone https://github.com/gawbul/pyEnsemblRest.git
cd pyEnsemblRest
make install

Usage

To import and setup a new EnsemblRest object you should do the following:

from pyensemblrest import EnsemblRest
ensRest = EnsemblRest()

The EnsemblRest() instance points to https://rest.ensembl.org/ by default.

To use a custom Ensembl REST server you should setup the EnsemblRest() as follows:

from pyensemblrest import EnsemblRest
# setup rest object to point to localhost server. The 3000 stands for REST default port
ensRest = EnsemblRest(base_url='http://localhost:3000')

You may also provide proxy server settings in the form of a dict, as follows:

from pyensemblrest import EnsemblRest
# setup rest object to point to a proxy server
ensRest = EnsemblRest(proxies={'http':'proxy.address.com:3128', 'https':'proxy.address.com:3128'})

EnsEMBL has a rate-limit policy to deal with requests. You can do up to 15 requests per second. You could wait a little during your requests:

from time import sleep
# sleep for a second so we don't get rate-limited
sleep(1)

Alternatively this library verifies and limits your requests to 15 requests per second. Avoid running different python processes to get your data, otherwise you will be blacklisted by the Ensembl team. If you have to do a lot or requests, consider using POST supported endpoints, or contact the Ensembl team to add POST support to endpoints of your interest.

GET endpoints

EnsemblRest class methods are not defined in the libraries so you cannot see docstrings using the help() method on the python or ipython terminal. However you can see all methods available for the ensembl REST server once the class is instantiated. To get help on a particular method, please refer to Ensembl help documentation for different endpoints in the Ensembl REST service. If you look at the sequence endpoint documentation, you will find optional and required parameters. Required parameters must be specified in order to work properly, otherwise you will get an exception. Optional parameters may be specified or not, depending on your request. In all cases parameter names are the same as those used in documentation. For example to get data using the sequence endpoint, you must specify at least the required parameters:

seq = ensRest.getSequenceById(id='ENSG00000157764')

In order to mask the sequence and to expand the 5' UTR you may set optional parameters using the same parameter described in the documentation:

seq = ensRest.getSequenceById(id='ENSG00000157764', mask="soft", expand_5prime=1000)

Multiple values for certain parameters (for GET methods) can be submitted in a list. For example, to get the same result for

curl 'http://rest.ensembl.org/overlap/region/human/7:140424943-140624564?feature=gene;feature=transcript;feature=cds;feature=exon' -H 'Content-type:application/json'

as described in overlap region GET endpoint, you can use the following function and parameters:

data = ensRest.getOverlapByRegion(species="human", region="7:140424943-140624564", feature=["gene", "transcript", "cds", "exon"])

POST endpoints

POST endpoints can be used as the GET endpoints, the only difference is that they support parameters in a python list in order to perform multiple queries on the same Ensembl endpoint. The parameter names are the same as used in the documentation, for example we can use the POST sequence endpoint in the following way:

seqs = ensRest.getSequenceByMultipleIds(ids=["ENSG00000157764", "ENSG00000248378"])

where the example values { "ids": ["ENSG00000157764", "ENSG00000248378"] } are converted to the non-positional argument ids=["ENSG00000157764", "ENSG00000248378"]. As with the previous example, we can add optional parameters:

seqs = ensRest.getSequenceByMultipleIds(ids=["ENSG00000157764", "ENSG00000248378"], mask="soft")

Change the default output format

You can change the default output format by passing a supported Content-type using the content_type parameter, for example:

plain_xml = ensRest.getArchiveById(id='ENSG00000157764', content_type="text/xml")

For a complete list of supported Content-type see Supported MIME Types from the Ensembl REST documentation. You also need to check if the same Content-type is supported in the EnsEMBL endpoint description.

Rate limiting

Sometime you can be rate limited if you are querying EnsEMBL REST services with more than one concurrent process, or by sharing ip addresses. In such case, you can receive a message like this:

ensemblrest.exceptions.EnsemblRestRateLimitError: EnsEMBL REST API returned a 429 (Too Many Requests): You have been rate-limited; wait and retry. The headers X-RateLimit-Reset, X-RateLimit-Limit and X-RateLimit-Remaining will inform you of how long you have until your limit is reset and what that limit was. If you get this response and have not exceeded your limit then check if you have made too many requests per second. (Rate limit hit:  Retry after 2 seconds)

Even though this library tries to do 15 request per seconds, you should avoid running multiple EnsEMBL REST clients. To deal which such problems without interrupting your code, try to deal with the exceptions; For example:

# import required modules
import os
import sys
import time
import logging

# get ensembl REST modules and exception
from pyensemblrest import EnsemblRest
from pyensemblrest import EnsemblRestRateLimitError

# An useful way to defined a logger lever, handler, and formatter
logging.basicConfig(format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', level=logging.INFO)
logger = logging.getLogger(os.path.basename(sys.argv[0]))

# setup a new EnsemblRest object
ensRest = EnsemblRest()

# Get a request and deal with retry_after. Set a maximum number of retries (don't
# try to do the same request forever or you will be banned from ensembl!)
attempt = 0
max_attempts = 3

while attempt < max_attempts:
    # update attempt count
    attempt += 1

    try:
        result = ensRest.getLookupById(id='ENSG00000157764')
        # exit while on success
        break

    # log exception and sleep a certain amount of time (sleeping time increases at each step)
    except EnsemblRestRateLimitError, message:
        logger.warn(message)
        time.sleep(ensRest.retry_after*attempt)

    finally:
        if attempt >= max_attempts:
            raise Exception("max attempts exceeded (%s)" %(max_attempts))

sys.stdout.write("%s\n" %(result))
sys.stdout.flush()

Methods list

Here is a list of all methods defined. Methods called by ensRest instance are specific to the Ensembl REST server.

To access the Archive endpoints you can use the following methods:

print(ensRest.getArchiveById(id="ENSG00000157764"))
print(ensRest.getArchiveByMultipleIds(id=["ENSG00000157764", "ENSG00000248378"]))

To access the Comparative Genomics endpoints you can use the following methods:

print(ensRest.getCafeGeneTreeById(id="ENSGT00390000003602"))
print(ensRest.getCafeGeneTreeMemberBySymbol(species="human", symbol="BRCA2"))
print(ensRest.getCafeGeneTreeMemberById(species="human", id="ENSG00000167664"))
print(ensRest.getGeneTreeById(id="ENSGT00390000003602"))
print(ensRest.getGeneTreeMemberBySymbol(species="human", symbol="BRCA2"))
print(ensRest.getGeneTreeMemberById(species="human", id="ENSG00000167664"))
print(
    ensRest.getAlignmentByRegion(
        species="human",
        region="X:1000000..1000100:1",
        species_set_group="mammals",
    )
)
print(ensRest.getHomologyById(species="human", id="ENSG00000157764"))
print(ensRest.getHomologyBySymbol(species="human", symbol="BRCA2"))

To access the Cross References endpoints you can use the following methods:

print(ensRest.getXrefsBySymbol(species="human", symbol="BRCA2"))
print(ensRest.getXrefsById(id="ENSG00000157764"))
print(ensRest.getXrefsByName(species="human", name="BRCA2"))

To access the Information endpoints you can use the following methods:

print(ensRest.getInfoAnalysis(species="homo_sapiens"))
print(
    ensRest.getInfoAssembly(species="homo_sapiens", bands=1)
)  # bands is an optional parameter
print(ensRest.getInfoAssemblyRegion(species="homo_sapiens", region_name="X"))
ensRest.timeout = 300
print(ensRest.getInfoBiotypes(species="homo_sapiens"))  # this keeps timing out
ensRest.timeout = 60
print(ensRest.getInfoBiotypesByGroup(group="coding", object_type="gene"))
print(ensRest.getInfoBiotypesByName(name="protein_coding", object_type="gene"))
print(ensRest.getInfoComparaMethods())
print(ensRest.getInfoComparaSpeciesSets(methods="EPO"))
print(ensRest.getInfoComparas())
print(ensRest.getInfoData())
print(ensRest.getInfoEgVersion())
print(ensRest.getInfoExternalDbs(species="homo_sapiens"))
print(ensRest.getInfoDivisions())
print(ensRest.getInfoGenomesByName(name="arabidopsis_thaliana"))
print(ensRest.getInfoGenomesByAccession(accession="U00096"))
print(ensRest.getInfoGenomesByAssembly(assembly_id="GCA_902167145.1"))
print(ensRest.getInfoGenomesByDivision(division="EnsemblPlants"))
print(ensRest.getInfoGenomesByTaxonomy(taxon_name="Homo sapiens"))
print(ensRest.getInfoPing())
print(ensRest.getInfoRest())
print(ensRest.getInfoSoftware())
print(ensRest.getInfoSpecies())
print(ensRest.getInfoVariationBySpecies(species="homo_sapiens"))
print(ensRest.getInfoVariationConsequenceTypes())
print(
    ensRest.getInfoVariationPopulationIndividuals(
        species="human", population_name="1000GENOMES:phase_3:ASW"
    )
)
# Restrict populations returned to e.g. only populations with LD data. It is highly recommended
# to set a filter and to avoid loading the complete list of populations.
print(ensRest.getInfoVariationPopulations(species="homo_sapiens", filter="LD"))

To access the Linkage Disequilibrium endpoints you can use the following methods:

print(
    ensRest.getLdId(
        species="homo_sapiens",
        id="rs56116432",
        population_name="1000GENOMES:phase_3:KHV",
        window_size=500,
        d_prime=1.0,
    )
)
print(ensRest.getLdPairwise(species="homo_sapiens", id1="rs6792369", id2="rs1042779"))
print(
    ensRest.getLdRegion(
        species="homo_sapiens",
        region="6:25837556..25843455",
        population_name="1000GENOMES:phase_3:KHV",
    )
)

To access the Lookup endpoints you can use the following methods:

print(ensRest.getLookupById(id="ENSG00000157764"))
print(ensRest.getLookupByMultipleIds(ids=["ENSG00000157764", "ENSG00000248378"]))
print(ensRest.getLookupBySymbol(species="homo_sapiens", symbol="BRCA2", expand=1))
print(
    ensRest.getLookupByMultipleSymbols(
        species="homo_sapiens", symbols=["BRCA2", "BRAF"]
    )
)

To access the Mapping endpoints you can use the following methods:

print(ensRest.getMapCdnaToRegion(id="ENST00000288602", region="100..300"))
print(ensRest.getMapCdsToRegion(id="ENST00000288602", region="1..1000"))
print(
    ensRest.getMapAssemblyOneToTwo(
        species="homo_sapiens",
        asm_one="GRCh37",
        region="X:1000000..1000100:1",
        asm_two="GRCh38",
    )
)
print(ensRest.getMapTranslationToRegion(id="ENSP00000288602", region="100..300"))

To access the Ontologies and Taxonomy endpoints you can use the following methods:

print(ensRest.getAncestorsById(id="GO:0005667"))
print(ensRest.getAncestorsChartById(id="GO:0005667"))
print(ensRest.getDescendantsById(id="GO:0005667"))
print(ensRest.getOntologyById(id="GO:0005667"))
print(ensRest.getOntologyByName(name="transcription factor complex"))
print(ensRest.getTaxonomyClassificationById(id="9606"))
print(ensRest.getTaxonomyById(id="9606"))
print(ensRest.getTaxonomyByName(name="Homo%25"))

To access the Overlap endpoints you can use the following methods:

print(ensRest.getOverlapById(id="ENSG00000157764", feature="gene"))
print(
    ensRest.getOverlapByRegion(
        species="homo_sapiens", region="X:1..1000:1", feature="gene"
    )
)
print(ensRest.getOverlapByTranslation(id="ENSP00000288602"))

To access the Phenotype annotations endpoints you can use the following methods:

print(ensRest.getPhenotypeByAccession(species="homo_sapiens", accession="EFO:0003900"))
print(ensRest.getPhenotypeByGene(species="homo_sapiens", gene="ENSG00000157764"))
print(
    ensRest.getPhenotypeByRegion(species="homo_sapiens", region="9:22125500-22136000:1")
)
print(ensRest.getPhenotypeByTerm(species="homo_sapiens", term="coffee consumption"))

To access the Regulation endpoints you can use the following method:

print(
    ensRest.getRegulationBindingMatrix(
        species="homo_sapiens", binding_matrix="ENSPFM0001"
    )
)

To access the Sequences endpoints you can use the following methods:

print(ensRest.getSequenceById(id="ENSG00000157764"))
print(ensRest.getSequenceByMultipleIds(ids=["ENSG00000157764", "ENSG00000248378"]))
print(
    ensRest.getSequenceByRegion(species="homo_sapiens", region="X:1000000..1000100:1")
)
print(
    ensRest.getSequenceByMultipleRegions(
        species="homo_sapiens",
        regions=["X:1000000..1000100:1", "ABBA01004489.1:1..100"],
    )
)

To access the Transcript Haplotypes endpoints you can use the following method:

print(ensRest.getTranscriptHaplotypes(species="homo_sapiens", id="ENST00000288602"))

To access the VEP endpoints you can use the following methods:

print(
    ensRest.getVariantConsequencesByHGVSNotation(
        species="homo_sapiens", hgvs_notation="ENST00000366667:c.803C>T"
    )
)
print(
    ensRest.getVariantConsequencesByMultipleHGVSNotations(
        species="homo_sapiens",
        hgvs_notations=["ENST00000366667:c.803C>T", "9:g.22125504G>C"],
    )
)
print(ensRest.getVariantConsequencesById(species="homo_sapiens", id="rs56116432"))
print(
    ensRest.getVariantConsequencesByMultipleIds(
        species="homo_sapiens", ids=["rs56116432", "COSM476", "__VAR(sv_id)__"]
    )
)
print(
    ensRest.getVariantConsequencesByRegion(
        species="homo_sapiens", region="9:22125503-22125502:1", allele="C"
    )
)
print(
    ensRest.getVariantConsequencesByMultipleRegions(
        species="homo_sapiens",
        variants=[
            "21 26960070 rs116645811 G A . . .",
            "21 26965148 rs1135638 G A . . .",
        ],
    )
)

To access the Variation endpoints you can use the following methods:

print(ensRest.getVariationRecoderById(species="homo_sapiens", id="rs56116432"))
print(
    ensRest.getVariationRecoderByMultipleIds(
        species="homo_sapiens", ids=["rs56116432", "rs1042779"]
    )
)
print(ensRest.getVariationById(species="homo_sapiens", id="rs56116432"))
print(ensRest.getVariationByPMCID(species="homo_sapiens", pmcid="PMC5002951"))
print(ensRest.getVariationByPMID(species="homo_sapiens", pmid="26318936"))
print(
    ensRest.getVariationByMultipleIds(
        species="homo_sapiens", ids=["rs56116432", "COSM476", "__VAR(sv_id)__"]
    )
)

To access the Variation GA4GH endpoints you can use the following methods:

print(ensRest.getGA4GHBeacon())
print(
    ensRest.getGA4GHBeaconQuery(
        alternateBases="C",
        assemblyId="GRCh38",
        end="23125503",
        referenceBases="G",
        referenceName="9",
        start="22125503",
        variantType="DUP",
    )
)
print(
    ensRest.postGA4GHBeaconQuery(
        alternateBases="C",
        assemblyId="GRCh38",
        end="23125503",
        referenceBases="G",
        referenceName="9",
        start="22125503",
        variantType="DUP",
    )
)
print(ensRest.getGA4GHFeaturesById(id="ENST00000408937.7"))
ensRest.timeout = 180
print(
    ensRest.searchGA4GHFeatures(
        parentId="ENST00000408937.7",
        featureSetId="",
        featureTypes=["cds"],
        end=220023,
        referenceName="X",
        start=197859,
        pageSize=1,
    )
)  # this keeps timing out
ensRest.timeout = 60
print(ensRest.searchGA4GHCallset(variantSetId=1, pageSize=2))
print(ensRest.getGA4GHCallsetById(id="1"))
print(ensRest.searchGA4GHDatasets(pageSize=3))
print(ensRest.getGA4GHDatasetsById(id="6e340c4d1e333c7a676b1710d2e3953c"))
print(ensRest.searchGA4GHFeaturesets(datasetId="Ensembl"))
print(ensRest.getGA4GHFeaturesetsById(id="Ensembl"))
print(ensRest.getGA4GHVariantsById(id="1:rs1333049"))
print(
    ensRest.searchGA4GHVariantAnnotations(
        variantAnnotationSetId="Ensembl",
        referenceId="9489ae7581e14efcad134f02afafe26c",
        start=25221400,
        end=25221500,
        pageSize=1,
    )
)
print(
    ensRest.searchGA4GHVariants(
        variantSetId=1,
        referenceName=22,
        start=25455086,
        end=25455087,
        pageToken="",
        pageSize=1,
    )
)
print(
    ensRest.searchGA4GHVariantsets(
        datasetId="6e340c4d1e333c7a676b1710d2e3953c", pageToken="", pageSize=2
    )
)
print(ensRest.getGA4GHVariantsetsById(id=1))
print(ensRest.searchGA4GHReferences(referenceSetId="GRCh38", pageSize=10))
print(ensRest.getGA4GHReferencesById(id="9489ae7581e14efcad134f02afafe26c"))
print(ensRest.searchGA4GHReferencesets())
print(ensRest.getGA4GHReferencesetsById(id="GRCh38"))
print(ensRest.searchGA4GHVariantAnnotationsets(variantSetId="Ensembl"))
print(ensRest.getGA4GHVariantAnnotationsetsById(id="Ensembl"))