pyEnsemblRest 0.1.7b

An easy way to access EnsEMBL data with Python.

pyEnsemblRest is a simple Python wrapper around the EnsEMBL REST API

Installation

git clone git://github.com/gawbul/pyensemblrest.git
cd pyensemblrest
sudo python setup.py install

Usage

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

from ensemblrest import EnsemblRest
ensemblrest = EnsemblRest()

To use a custom EnsEMBL REST server you should setup the EnsemblRest object as follows:

from ensemblrest import EnsemblRest
ensemblrest = EnsemblRest(server='localhost') # setup rest object to point to localhost server

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

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

You should also sleep for a second between every 3 requests (with bursts of 6 requests allowed periodically) using the following syntax:

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

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

print ensemblrest.getGeneTreeById(id='ENSGT00390000003602')
print ensemblrest.getGeneTreeByMemberId(id='ENSG00000157764')
print ensemblrest.getGeneTreeByMemberSymbol(species='human', symbol='BRCA2')
print ensemblrest.getHomologyById(id='ENSG00000157764')
print ensemblrest.getHomologyBySymbol(species='human', symbol='BRCA2')

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

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

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

print ensemblrest.getFeatureById(id='ENSG00000157764', feature='gene')
print ensemblrest.getFeatureByRegion(species='human', region='7:140424943..140624564', feature='gene')

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

print ensemblrest.getAssemblyInfo(species='human')
print ensemblrest.getAssemblyInfoRegion(species='human', region_name='X')
print ensemblrest.getInfoComparas()
print ensemblrest.getInfoData()
print ensemblrest.getInfoPing()
print ensemblrest.getInfoRest()
print ensemblrest.getInfoSoftware()
print ensemblrest.getInfoSpecies()

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

print ensemblrest.getLookupById(id='ENSG00000157764')

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

print ensemblrest.getMapAssemblyOneToTwo(species='human', asm_one='NCBI36', region='X:1000000..1000100:1', asm_two='GRCh37')
print ensemblrest.getMapCdnaToRegion(id='ENST00000288602', region='100..300')
print ensemblrest.getMapCdsToRegion(id='ENST00000288602', region='1..1000')
print ensemblrest.getMapTranslationToRegion(id='ENSP00000288602', region='100..300')

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

print ensemblrest.getAncestorsById(id='GO:0005667')
print ensemblrest.getAncestorsChartById(id='GO:0005667')
print ensemblrest.getDescendentsById(id='GO:0005667')
print ensemblrest.getOntologyById(id='GO:0005667')
print ensemblrest.getOntologyByName(name='transcription factor complex')
print ensemblrest.getTaxonomyClassificationById(id='9606')
print ensemblrest.getTaxonomyById(id='9606')

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

print ensemblrest.getSequenceById(id='ENSG00000157764')
print ensemblrest.getSequenceByRegion(species='human', region='X:1000000..1000100')

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

print ensemblrest.getVariantConsequencesByRegion(species='human', region='9:22125503-22125502:1', allele='C')
print ensemblrest.getVariantConsequencesById(species='human', id='COSM476')