Metadata-Version: 1.2
Name: bioservices
Version: 1.8.0
Summary: Access to Biological Web Services from Python
Home-page: http://github.com/cokelaer/bioservices
Author: Thomas Cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: Thomas Cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: GPLv3
Download-URL: http://pypi.python.org/pypi/bioservices
Description: #################################################################################
        BIOSERVICES: access to biological web services programmatically
        #################################################################################
        
        
        .. image:: https://badge.fury.io/py/bioservices.svg
            :target: https://pypi.python.org/pypi/bioservices
        
        .. image:: https://github.com/cokelaer/bioservices/actions/workflows/ci.yml/badge.svg
           :target: https://github.com/cokelaer/bioservices/actions/workflows/ci.yml
        
        .. image:: http://readthedocs.org/projects/bioservices/badge/?version=master
            :target: http://bioservices.readthedocs.org/en/master/?badge=master
            :alt: Documentation Status
        
        .. image:: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png
            :target: https://raw.githubusercontent.com/cokelaer/bioservices/master/doc/bioservices.png
        
        :Python_version_available: BioServices is tested for Python 3.6, 3.7, 3.8
        :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).
        
        
        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 about 40 Web Services. 
        
        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 `On-line documentation <http://bioservices.readthedocs.io/>`_
        
        Here is the list of services available and their testing status.
        
        
        ==================== ================================================================================================
        Service              CI testing
        ==================== ================================================================================================
        arrayexpress          .. image:: https://github.com/cokelaer/bioservices/actions/workflows/arrayexpress.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/arrayexpress.yml
        bigg                  .. image:: https://github.com/cokelaer/bioservices/actions/workflows/bigg.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/bigg.yml
        biocarta              .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biocarta.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/biocarta.yml
        biodbnet              .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biodbnet.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/biodbnet.yml
        biogrid               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biogrid.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/biogrid.yml
        biomart               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biomart.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/biomart.yml
        biomodels             .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biomodels.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/biomodels.yml
        chebi                 .. image:: https://github.com/cokelaer/bioservices/actions/workflows/chebi.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/chebi.yml
        chembl                .. image:: https://github.com/cokelaer/bioservices/actions/workflows/chembl.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/chembl.yml
        cog                   .. image:: https://github.com/cokelaer/bioservices/actions/workflows/cog.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/cog.yml
        dbfetch               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/dbfetch.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/dbfetch.yml
        ena                   .. image:: https://github.com/cokelaer/bioservices/actions/workflows/ena.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/ena.yml
        ensembl               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/ensembl.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/ensembl.yml
        eutils                .. image:: https://github.com/cokelaer/bioservices/actions/workflows/eutils.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/eutils.yml
        eva                   .. image:: https://github.com/cokelaer/bioservices/actions/workflows/eva.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/eva.yml
        hgnc                  .. image:: https://github.com/cokelaer/bioservices/actions/workflows/hgnc.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/hgnc.yml
        intact_complex        .. image:: https://github.com/cokelaer/bioservices/actions/workflows/intact_complex.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/intact_complex.yml
        kegg                  .. image:: https://github.com/cokelaer/bioservices/actions/workflows/kegg.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/kegg.yml
        muscle                .. image:: https://github.com/cokelaer/bioservices/actions/workflows/muscle.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/muscle.yml
        mygeneinfo            .. image:: https://github.com/cokelaer/bioservices/actions/workflows/mygeneinfo.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/mygeneinfo.yml
        ncbiblast             .. image:: https://github.com/cokelaer/bioservices/actions/workflows/ncbiblast.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/ncbiblast.yml
        omicsdi               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/omicsdi.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/omicsdi.yml
        omnipath              .. image:: https://github.com/cokelaer/bioservices/actions/workflows/omnipath.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/omnipath.yml
        panther               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/panther.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/panther.yml
        pathwaycommons        .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pathwaycommons.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/pathwaycommons.yml
        pdb                   .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pdb.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/pdb.yml
        pdbe                  .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pdbe.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/pdbe.yml
        pfam                  .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pfam.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/pfam.yml
        pride                 .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pride.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/pride.yml
        psicquic              .. image:: https://github.com/cokelaer/bioservices/actions/workflows/psicquic.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/psicquic.yml
        pubchem               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/pubchem.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/pubchem.yml
        quickgo               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/quickgo.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/quickgo.yml
        reactome              .. image:: https://github.com/cokelaer/bioservices/actions/workflows/reactome.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/reactome.yml
        rhea                  .. image:: https://github.com/cokelaer/bioservices/actions/workflows/rhea.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/rhea.yml
        rnaseq_ebi            .. image:: https://github.com/cokelaer/bioservices/actions/workflows/rnaseq_ebi.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/rnaseq_ebi.yml
        seqret                .. image:: https://github.com/cokelaer/bioservices/actions/workflows/seqret.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/seqret.yml
        unichem               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/unichem.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/unichem.yml
        uniprot               .. image:: https://github.com/cokelaer/bioservices/actions/workflows/uniprot.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/uniprot.yml
        wikipathway           .. image:: https://github.com/cokelaer/bioservices/actions/workflows/wikipathway.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/wikipathway.yml
        ==================== ================================================================================================
        
        
        .. note:: Contributions to implement new wrappers are more than welcome. 
            See `BioServices github page <https://github.com/cokelaer/bioservices/>`_
            to join the development, and the Developer guide on how to implement new
            wrappers.
        
        
        ========= ====================================================================
        Version   Description
        ========= ====================================================================
        1.8.0     * add main standalone application. 
                  * moved chemspider and clinvitae to the attic
                  * removed picr service, not active anymore
        ========= ====================================================================
        
        
        
        
        
        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
        
        
Keywords: BioServices,WebServices,Biology,BioDBNet,ChEBI,UniChem,Kegg,KEGG,BioModels,EUtils,UniProt,PICR,ArrayExpress,MUSCLE,QuickGO,PDB,PSICQUIC,Blast,BioMART,PantherDB,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 General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
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
