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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:

.. code:: bash

pip install pyensemblrest

From source

Clone the pyEnsemblRest then install package from source:

.. code:: bash

git clone https://github.com/pyOpenSci/pyEnsemblRest.git cd pyEnsemblRest sudo python setup.py install

Usage

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

.. code:: python

from ensemblrest import EnsemblRest ensRest = EnsemblRest()

EnsemblRest() istance points to http://rest.ensembl.org/ . In order to use EnsemblGenome, you can import a different object:

.. code:: python

from ensemblrest import EnsemblGenomeRest ensGenomeRest = EnsemblGenomeRest()

Or, as an alternative, you can give a different base url during EnsemblRest class instantiation:

.. code:: python

from ensemblrest import EnsemblRest ensGenomeRest = EnsemblRest(base_url='http://rest.ensemblgenomes.org')

To use a custom EnsEMBL REST server you should setup the EnsemblRest as the precedent way:

.. code:: python

from ensemblrest 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:

.. code:: python

from ensemblrest 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:

.. code:: python

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 to run different python processes to get your data, otherwise you will be blacklisted by ensembl team. If you have to do a lot or requests, consider to use POST supported endpoints, or contact ensembl team to add POST support to endpoints of your interest.

GET endpoints

EnsemblRest and EnsemblGenomeRest class methods are not defined in libraries, so you cannot see docstring using help() method on python or ipython terminal. However you can see all methods available for ensembl_ and ensemblgenomes_ rest server once class is instantiate. To get help on a particular method, please refer to ensembl help documentation on different endpoints in the ensembl_ and ensemblgenomes_ rest service. Please note that endpoints on ensembl_ may be different from ensemblgenomes_ endpoints. If you look, for example, at 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 name are the same used in documentation. For example to get data using sequence_ endpoint, you must specify at least required parameters:

.. code:: python

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

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

.. code:: python

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

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

.. code:: bash

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:

.. code:: python

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

.. _overlap region: http://rest.ensembl.org/documentation/info/overlap_region

POST endpoints

POST endpoints can be used as the GET endpoints, the only difference is that they support parameters in python list in order to perform multiple queries on the same ensembl endpoint. The parameters name are the same used in documentation, for example we can use the POST sequence_ endpoint in such way:

.. code:: python

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

where the example value { "ids" : ["ENSG00000157764", "ENSG00000248378" ] } is converted in the non-positional argument ids=["ENSG00000157764", "ENSG00000248378" ]. As the previous example, we can add optional parameters:

.. code:: python

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:

.. code:: python

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

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

.. _Supported MIME Types: https://github.com/Ensembl/ensembl-rest/wiki/Output-formats#supported-mime-types

Rate limiting

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

.. _sharing ip addresses: https://github.com/Ensembl/ensembl-rest/wiki#example-clients

.. code:: bash

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 if this library tries to do 15 request per seconds, you should avoid to run multiple EnsEMBL REST clients. To deal which such problem without interrupting your code, try to deal with the exception; For example:

.. code:: python

import required modules

import os import sys import time import logging

get ensembl REST modules and exception

from ensemblrest import EnsemblRest from ensemblrest 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 ensembl_ rest server, while methods called via ensGenomeRest instance are specific of ensemblgenomes_ rest server.

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

.. code:: python

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

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

.. code:: python

print ensGenomeRest.getGeneFamilyById(id="MF_01687", compara="bacteria") print ensGenomeRest.getGeneFamilyMemberById(id="b0344", compara="bacteria") print ensGenomeRest.getGeneFamilyMemberBySymbol(symbol="lacZ", species="escherichia_coli_str_k_12_substr_mg1655", compara="bacteria")

Change the returned content type to "Newick" format

print ensRest.getGeneTreeById(id='ENSGT00390000003602', nh_format="simple", content_type="text/x-nh") print ensRest.getGeneTreeMemberById(id='ENSG00000157764') print ensRest.getGeneTreeMemberBySymbol(species='human', symbol='BRCA2') print ensRest.getAlignmentByRegion(species="taeniopygia_guttata", region="2:106040000-106040050:1", species_set_group="sauropsids") print ensRest.getHomologyById(id='ENSG00000157764') print ensRest.getHomologyBySymbol(species='human', symbol='BRCA2')

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

.. code:: python

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

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

.. code:: python

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") print ensRest.getInfoBiotypes(species="homo_sapiens") print ensRest.getInfoComparaMethods() print ensRest.getInfoComparaSpeciesSets(methods="EPO") print ensRest.getInfoComparas() print ensRest.getInfoData() print ensGenomeRest.getInfoEgVersion() print ensRest.getInfoExternalDbs(species="homo_sapiens") print ensGenomeRest.getInfoDivisions() print ensGenomeRest.getInfoGenomesByName(name="campylobacter_jejuni_subsp_jejuni_bh_01_0142")

#This response is very heavy #print ensGenomeRest.getInfoGenomes()

print ensGenomeRest.getInfoGenomesByAccession(division="U00096") print ensGenomeRest.getInfoGenomesByAssembly(division="GCA_000005845") print ensGenomeRest.getInfoGenomesByDivision(division="EnsemblPlants") print ensGenomeRest.getInfoGenomesByTaxonomy(division="Arabidopsis") print ensRest.getInfoPing() print ensRest.getInfoRest() print ensRest.getInfoSoftware() print ensRest.getInfoSpecies(division="ensembl") print ensRest.getInfoVariation(species="homo_sapiens")

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:

.. code:: python

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

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

.. code:: python

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:

.. code:: python

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

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

.. code:: python

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:

.. code:: python

print ensRest.getOverlapById(id="ENSG00000157764", feature="gene") print ensRest.getOverlapByRegion(species="human", region="7:140424943-140624564", feature="gene") print ensRest.getOverlapByTranslation(id="ENSP00000288602")

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

.. code:: python

print ensRest.getRegulatoryFeatureById(species="homo_sapiens", id="ENSR00001348195")

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

.. code:: python

print ensRest.getSequenceById(id='ENSG00000157764') print ensRest.getSequenceByMultipleIds(ids=["ENSG00000157764", "ENSG00000248378" ]) print ensRest.getSequenceByRegion(species='human', region='X:1000000..1000100') 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 methods:

.. code:: python

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

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

.. code:: python

print ensRest.getVariantConsequencesByHGVSnotation(species="human", hgvs_notation="AGT:c.803T>C") print ensRest.getVariantConsequencesById(species='human', id='COSM476') print ensRest.getVariantConsequencesByMultipleIds(species="human", ids=[ "rs116035550", "COSM476" ]) print ensRest.getVariantConsequencesByRegion(species='human', region='9:22125503-22125502:1', allele='C') print ensRest.getVariantConsequencesByMultipleRegions(species="human", variants=["21 26960070 rs116645811 G A . . .", "21 26965148 rs1135638 G A . . ." ] )

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

.. code:: python

print ensRest.getVariationById(id="rs56116432", species="homo_sapiens") print ensRest.getVariationByMultipleIds(ids=["rs56116432", "COSM476" ], species="homo_sapiens")

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

.. code:: python

print ensRest.searchGA4GHCallSet(variantSetId=1, pageSize=2) print ensRest.getGA4GHCallSetById(id="1:NA19777") print ensRest.searchGA4GHDataset(pageSize=3) print ensRest.getGA4GHDatasetById(id="6e340c4d1e333c7a676b1710d2e3953c") print ensRest.getGA4GHVariantsById(id="1:rs1333049") print ensRest.searchGA4GHVariants(variantSetId=1, referenceName=22, start=17190024, end=17671934, 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")

.. _ensembl: http://rest.ensembl.org/ .. _ensemblgenomes: http://rest.ensemblgenomes.org/ .. _sequence: http://rest.ensembl.org/documentation/info/sequence_id .. _POST sequence: http://rest.ensembl.org/documentation/info/sequence_id_post

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