An easy way to access EnsEMBL data with Python.
Project description
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')
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