Metadata-Version: 1.1
Name: bioservices
Version: 1.3.4
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
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        .. 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.
        
        :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
        
        **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>`_
        * ChEMBL on `chembl nbviewer <http://nbviewer.ipython.org/url/pythonhosted.org//bioservices/_downloads/ChEMBL.ipynb>`_
        * Ensembl on `Ensembl nbviewer <https://github.com/bioservices/notebooks/tree/master/ensembl>`_
        * 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 `nbviewer <http://nbviewer.ipython.org/github/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 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", 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>`_
        
        
        
        
        Release History
        ------------------
        This is a summary of the changelog. Complete change can be found in the 
        `main documentation <http://pythonhosted.org//bioservices/ChangeLog.html>`_.
        
        1.3.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 ...
        
        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>`_.
        
        1.3.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
        
        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
        
        
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,Ensembl
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
