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Access to Biological Web Services from Python

Project description

BioServices
##############

.. image:: https://badge.fury.io/py/bioservices.svg
:target: https://pypi.python.org/pypi/bioservices

.. image:: https://secure.travis-ci.org/cokelaer/bioservices.png
:target: http://travis-ci.org/cokelaer/bioservices

.. image:: https://coveralls.io/repos/cokelaer/bioservices/badge.png?branch=master
:target: https://coveralls.io/r/cokelaer/bioservices?branch=master

.. image:: http://readthedocs.org/projects/bioservices/badge/?version=master
:target: http://bioservices.readthedocs.org/en/master/?badge=master
:alt: Documentation Status


:Python version available: BioServices is tested for Python 2.7, 3.3, 3.4, 3.5
:Contributions: Please join https://github.com/cokelaer/bioservices and share your notebooks https://github.com/bioservices/notebooks/
:Issues: Please use https://github.com/cokelaer/bioservices/issues
:How to cite: Cokelaer et al. *BioServices: a common Python package to access biological Web Services programmatically*
`Bioinformatics <http://bioinformatics.oxfordjournals.org/content/29/24/3241>`_ (2013) 29 (24): 3241-3242
:Documentation: `RTD documentation <http://bioservices.readthedocs.io/>`_.

**Bioservices** is a Python package that provides access to many Bioinformatices Web Services (e.g.,
UniProt) and a framework to easily implement Web Services wrappers (based on
WSDL/SOAP or REST protocols).

.. image:: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png
:target: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png


The primary goal of **BioServices** is to use Python as a glue language to provide
a programmatic access to several Bioinformatics Web Services. By doing so, elaboration of new
applications that combine several of the wrapped Web Services is fostered.

One of the main philosophy of **BioServices** is to make use of the existing
biological databases (not to re-invent new databases) and to alleviates the
needs for expertise in Web Services for the developers/users.

BioServices provides access to 25 Web Services including. For a quick start,
look at some notebooks here `github cokelaer/bioservices <https://github.com/cokelaer/bioservices/tree/master/notebooks/>`_ and here `github bioservices <https://github.com/bioservices/notebooks>`_.

An up-to-date list of Web Services is provided within
the online `documentation <http://pythonhosted.org/bioservices/>`_.

Here is a small example using the UniProt Web Service to search for the zap70 specy in human
organism::

>>> from bioservices import UniProt
>>> u = UniProt(verbose=False)
>>> data = u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3,
... columns="entry name,length,id, genes")
>>> print(data)
Entry name Length Entry Gene names
ZAP70_HUMAN 619 P43403 ZAP70 SRK
B4E0E2_HUMAN 185 B4E0E2
RHOH_HUMAN 191 Q15669 RHOH ARHH TTF

More examples and tutorials are available in the exhaustive
`On-line documentation <http://pythonhosted.org//bioservices>`_




Release History
------------------
This is a summary of the changelog. Complete change can be found in the
`main documentation <http://pythonhosted.org//bioservices/ChangeLog.html>`_.

1.5.X
---------

* Support for Python 3.6 on Travis.
* No more support for PYthon 2.6
* biodbnet and wikipathways services now uses the REST protocol (instead of
WSDL).
* move readseq to seqret and uses new EBI API
* move wsdbfetch to dbfetch (and switch to REST protocol)
* quickgo uses the new API from EBI
* For developers: use pytest instead of nosetests.




1.4.X
---------------

* Update uniprot valid column names.
* Renamed kegg.KEGG.info into dbinfo , which was overloaded with Logging
* Replaced deprecated HGNC with the official web service from genenames.org
* Fully updated EUtils since WSDL is now down; implementation uses REST now.
* Removed the apps/taxonomy module now part of http://github.com/biokit.
* added http_delete in services.py





1.3.X
+++++++++++

* Source code moved to github.com
* New REST class to use **requests** package instead of urllib2.
* Creation of a global configuration file in .config/bioservice/bioservices.cfg
* NEW services: Reactome, Readseq, Ensembl, EUtils, PRIDE, clinvitae, Intact
(complex)
* CHANGES: all parameters called format have been renamed frmt (to avoid using Python keyword)

1.2.X
+++++++++++

* add try/except for pandas library.
* added sub-package called apps with some useful tools (fasta,peptides, taxon) in bioservices.apps directory
* NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf

1.1.X
+++++++++++
* NEW services: biocarta, pfam, ChEBI, UniChem
* Add documentation and examples related to Galaxy/BioPython.
* NEW Service : HGNC
* Use BeautifulSoup4 instead of 3

1.0.X
+++++++++++
* add PDB, ArrayExpress, biomart, chemspider draft, eutils, miriam, arrayexpress

1.0.0
++++++

* First release of bioservices including the following services:
BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt,
WSDbfetch, NCBIblast, PSICQUIC, Wikipath



Release History
------------------
This is a summary of the changelog. Complete change can be found in the
`<main documentation <http://pythonhosted.org//bioservices/ChangeLog.html>`_.




1.4.X
---------------

* Include RNASEQ (EBI) in module rnaseq_ebi
* Renamed kegg.KEGG.info into dbinfo , which was overloaded with Logging
* Replaced deprecated HGNC with the official web service from genenames.org
* Fully updated EUtils since WSDL is now down; implementation uses REST now.
* Removed the apps/taxonomy module now part of http://github.com/biokit.
* added http_delete in services.py



1.3.X
+++++++++++

* CACHE files are now stored in a general directory in the home, rather than
locally
* Source code moved to github.com
* New REST class to use **requests** package instead of urllib2.
* Creation of a global configuration file in .config/bioservice/bioservices.cfg
* NEW services: Reactome, Readseq, Ensembl, EUtils

1.2.X
+++++++++++

* add try/except for pandas library.
* added sub-package called apps with some useful tools (fasta,peptides, taxon) in bioservices.apps directory
* NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf

1.1.X
+++++++++++
* NEW services: biocarta, pfam, ChEBI, UniChem
* Add documentation and examples related to Galaxy/BioPython.
* NEW Service : HGNC
* Use BeautifulSoup4 instead of 3

1.0.X
+++++++++++
* add PDB, ArrayExpress, biomart, chemspider draft, eutils, miriam, arrayexpress

1.0.0:
+++++++++++
* First release of bioservices


0.9.X:
+++++++++++
* Stable version of bioservices including the following services:
BioModels, Kegg, Reactome, Chembl, PICR, QuickGO, Rhea, UniProt,
WSDbfetch, NCBIblast, PSICQUIC, Wikipath

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