Metadata-Version: 1.1
Name: bioservices
Version: 1.3.1
Summary: Access to Biological Web Services from Python
Home-page: ['http://pypi.python.org/pypi/bioservices']
Author: Thomas Cokelaer
Author-email: cokelaer@ebi.ac.uk
License: GPL
Download-URL: ['http://pypi.python.org/pypi/bioservices']
Description: BioServices
        ##############
        
        .. image:: https://badge.fury.io/py/bioservices.svg
            :target: https://pypi.python.org/pypi/bioservices
        
        .. image:: https://pypip.in/d/bioservices/badge.png
            :target: https://crate.io/packages/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:: https://landscape.io/github/cokelaer/bioservices/master/landscape.png
           :target: https://landscape.io/github/cokelaer/bioservices/master
        
        .. image:: https://badge.waffle.io/cokelaer/bioservices.png?label=ready&title=Ready 
           :target: https://waffle.io/cokelaer/bioservices
        
        :note: BioServices is tested for Python 2.7, 3.3. Version 3.4 is currently not
               available due to a gevent dependencies, which should be fixed soon.
               Building may appear to fail sometimes but this is due to one or two services amongst 25 being
               down temporarily and is independent of BioServices. Similarly the
               coverage is actually higher than what is reported here above, which is
               a subset of the tests available for developers.
        
        
        **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:: http://pythonhosted.org//bioservices/_images/bioservices.png
            :target: http://pythonhosted.org//bioservices/_images/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 related to 
        
        * UniProt on `uniprot nbviewer <http://nbviewer.ipython.org/url/pythonhosted.org//bioservices/_downloads/UniProt.ipynb>`_
        * BioModels on `biomodels nbviewer <http://nbviewer.ipython.org/url/pythonhosted.org//bioservices/_downloads/BioModels.ipynb>`_
        * ChhEMBL on `chembl nbviewer <http://nbviewer.ipython.org/url/pythonhosted.org//bioservices/_downloads/ChEMBL.ipynb>`_
        * KEGG on `KEGG nbviewer <http://nbviewer.ipython.org/url/pythonhosted.org/bioservices/_downloads/KEGG.ipynb>`_
        * MUSCLE on `MUSCLE  nbviewer <http://nbviewer.ipython.org/url/pythonhosted.org/bioservices/_downloads/MUSCLE.ipynb>`_
        * NCBIBlast on `ncbiblast nbviewer <http://nbviewer.ipython.org/url/pythonhosted.org/bioservices/_downloads/NCBIBlast.ipynb>`_
        * WikiPathway on `wikipathway nbviewer <http://nbviewer.ipython.org/url/pythonhosted.org/bioservices/_downloads/WikiPathway.ipynb>`_
        
        and more on `github <https://github.com/cokelaer/bioservices/tree/master/doc/source/notebook>`_.
        
        An up-to-date list of Web Services is provided within 
        the online `documentation <http://pythonhosted.org/bioservices/>`_.
        
        Here is a little 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", format="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>`_
        
        
        .. :changelog:
        
        Relase History
        ------------------
        This is a summary of the changelog, which can be found in the main
        documentation.
        
        1.3.0
        +++++++++++
        
        * Source code moved to github.com
        * New REST class to use requests package instead of urllib2
        
        1.2.X
        +++++++++++
        
        * add try/except for pandas library.
        * fixing typo in the init that fails bioservices ito be used if pkg_resources is not available.
        * added sub-package called apps with some useful tools (fasta,peptides, taxon) in bioservices.apps directory
        * NEW the BioDBnet service.
        * NEW Pathway Common
        * NEW Service: :class:`bioservices.biodbnet.BioDBNet`
        * Kegg class has now an alias called KEGG
        * NEW Services: :class:`bioservices.muscle.MUSCLE`
        * NEW Service: :class:`bioservices.pathwaycommons.PathwayCommons`
        * NEW Service: :class:`bioservices.geneprof.GeneProf` service
        
        1.1.X
        +++++++++++ 
        * add biocarta, pfam modules (and htmltools. maybe not required.)
        * add documentation and examples related to Galaxy/BioPython.
        * NEW Service : class:`bioservices.hgnc.HGNC` + doc + test
        * Use BeautifulSoup4 instead of 3
        * add the ChEBI  Web Service.
        * add the UniChem  Web Service.
        
        1.0.X
        +++++++++++ 
        * add PDB
        * add ArrayExpress
        * add biomart + doc + test
        * add chemspider draft
        * complete eutils 
        * Add miriam module
        * Add 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
        
        
Keywords: BioServices,WebServices,Biology,BioDBNet,ChEBI,UniChem,Kegg,KEGG,BioModels,EUtils,UniProt,PICR,ArrayExpress,MUSCLE,QuickGO,PDB,PSICQUIC,Blast,BioMART,BioGRID,MIRIAM,BioMart,GeneProf,ChEMBL,ChemSpider,HGNC,PathwayCommons,Rhea
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU Library or Lesser General Public License (LGPL)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
