ensembl-rest 0.1.3

An interface to the Ensembl REST APIs, biological data at your fingertips.

EnsemblRest

A Python interface to the Ensembl REST APIs. A whole world of biological data at your fingertips.

The Ensembl database contains reference biological data on almost any organism. Now it is easy to access this data programatically through their REST API.

The specific documentation on the Ensembl REST API endpoints is on their website.

This library also includes some utilities built on top of the APIs designed to ease working with them, including an AssemblyMapper class that helps in the conversion between different genome assemblies.

This project uses code from RESTEasy, which made my life much easier. Thanks!

Installation

You can install from PyPI:

$ pip install ensembl_rest

Examples

The library exports two main classes: ensembl_rest.EnsemblClient and ensembl_rest.EnsemblGenomesClient that point respectively to the main REST API and to the Ensembl Genomes REST API.

>>> import ensembl_rest

>>> client = ensembl_rest.EnsemblClient()

If you want to use a method from the REST API, say: GET lookup/symbol/:species/:symbol (http://rest.ensembl.org/documentation/info/symbol_lookup) then the corresponding method on the class is called after the last string in the link to the documentation page, in this case, symbol_lookup.

>>> help(client.symbol_lookup)

Help on method symbol_lookup in module ensembl_rest.core.baseclient:

symbol_lookup(*args, **kwargs) method of ensembl_rest.core.baseclient.EnsemblClient instance
    ``GET lookup/symbol/:species/:symbol``

    Find the species and database for a symbol in a linked external database
    - More info: https://rest.ensembl.org/documentation/info/symbol_lookup

We can see from the resource string GET lookup/symbol/:species/:symbol that this method contains 2 parameters called species and symbol, so we can call the method in the following way:

>>> client.symbol_lookup(species='homo sapiens',
                         symbol='TP53')

# Or like this...
>>> client.symbol_lookup('homo sapiens', 'TP53')

{'source': 'ensembl_havana',
 'object_type': 'Gene',
 'logic_name': 'ensembl_havana_gene',
 'version': 16,
 'species': 'homo sapiens',
 'description': 'tumor protein p53 [Source:HGNC Symbol;Acc:HGNC:11998]',
 'display_name': 'TP53',
 'assembly_name': 'GRCh38',
 'biotype': 'protein_coding',
 'end': 7687550,
 'seq_region_name': '17',
 'db_type': 'core',
 'strand': -1,
 'id': 'ENSG00000141510',
 'start': 7661779}

Another common usage is to fetch sequences of known genes:

>>> client.sequence_id('ENSG00000157764')

{'desc': 'chromosome:GRCh38:7:140719327:140924928:-1',
 'query': 'ENSG00000157764',
 'version': 13,
 'id': 'ENSG00000157764',
 'seq': 'TTCCCCCAATCCCCTCAGGCTCGGCTGCGCCCGGGGC...ACTGCTATAATAAAGATTGACTGCATGGAGAAGTCTTCA',
 'molecule': 'dna'}

Or to map betweeen assemblies…

>>> client.assembly_map(species='human',
                        asm_one='GRCh37',
                        region='X:1000000..1000100:1',
                        asm_two='GRCh38')


# Or...
>>> region_str = ensembl_rest.region_str(chom='X',
                                         start=1000000,
                                         end=1000100)

>>> client.assembly_map(species='human',
                        asm_one='GRCh37',
                        region=region_str,
                        asm_two='GRCh38')

{'mappings': [{'original': {'seq_region_name': 'X',
    'strand': 1,
    'coord_system': 'chromosome',
    'end': 1000100,
    'start': 1000000,
    'assembly': 'GRCh37'},
   'mapped': {'seq_region_name': 'X',
    'strand': 1,
    'coord_system': 'chromosome',
    'end': 1039365,
    'start': 1039265,
    'assembly': 'GRCh38'}}]}

The above problem (mapping from one assembly to another) is so frequent that the library provides a specialized class AssemblyMapper to efficiently mapping large amounts of regions between assemblies. This class avoids the time-consuming task of making a web request every time a mapping is needed by fetching the mapping of the whole assembly right from the instantiation. This is a time-consuming operation by itself, but it pays off when one has to transform repeatedly betweeen assemblies.:

>>> mapper = ensembl_rest.AssemblyMapper(from_assembly='GRCh37'
...                                      to_assembly='GRCh38')

>>> mapper.map(chrom='1', pos=1000000)
1064620

Meta

Author: Ad115 - Github – [e-mail]

Distributed under the MIT license. See LICENSE for more information.

Contributing

1. Check for open issues or open a fresh issue to start a discussion around a feature idea or a bug.

2. Fork the repository on GitHub to start making your changes to a feature branch, derived from the master branch.

3. Write a test which shows that the bug was fixed or that the feature works as expected.

4. Send a pull request and bug the maintainer until it gets merged and published.