Metadata-Version: 1.1
Name: pyensemblrest
Version: 0.1.7b
Summary: An easy way to access EnsEMBL data with Python.
Home-page: http://github.com/pyopensci/pyensemblrest/tree/master
Author: Steve Moss
Author-email: gawbul@gmail.com
License: GPLv3
Description: =============
        pyEnsemblRest
        =============
        
        ``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')
Keywords: ensembl python rest api
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Internet
