Metadata-Version: 2.1
Name: bioservices
Version: 1.10.4
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=main
            :target: http://bioservices.readthedocs.org/en/main/?badge=main
            :alt: Documentation Status
        
        .. image:: https://static.pepy.tech/personalized-badge/bioservices?period=month&units=international_system&left_color=black&right_color=orange&left_text=Downloads
            :target: https://pepy.tech/project/bioservices
        
        .. image:: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_logo_256.png
            :target: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_logo_256.png
        
        
        :Python_version_available: BioServices is tested for Python 3.7, 3.8, 3.9, 3.10
        :Contributions: Please join https://github.com/cokelaer/bioservices 
        :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. 
        
        Contributors
        ============
        
        Maintaining BioServices would not have been possible without users and contributors. 
        Each contribution has been an encouragement to pursue this project. Thanks to all:
        
        .. image:: https://contrib.rocks/image?repo=cokelaer/bioservices
            :target: https://github.com/cokelaer/bioservices/graphs/contributors
        
        
        Quick example
        =============
        
        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_id:9606", frmt="tsv", limit=3, 
            ...                 columns="id,length,accession, gene_names")
            >>> 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
        
        
        .. note:: major changes of UniProt API changed all columns names in June 2022. The code above is valid for bioservices
           versions >1.10. Earlier version used::
        
                >>> data = u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3, 
                ...                 columns="entry name,length,id, genes")
        
           Note that columns names have changed, the frmt was changed from tab to tsv 
           and taxonomy is now taxonomy_id. Names correspondences can be found in::
        
                u._legacy_names
        
        
        More examples and tutorials are available in the `On-line documentation <http://bioservices.readthedocs.io/>`_
        
        Current services
        ================
        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
        biocontainers         .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biocontainers.yml/badge.svg
                                 :target: https://github.com/cokelaer/bioservices/actions/workflows/biocontainers.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.
        
        Bioservices command
        ====================
        
        In version 1.8.2, we included a bioservices command. For now it has only one subcommand to download a NCBI accession number and possibly it genbank or GFF file (if available)::
        
            bioservices download-accession --accession K01711.1 --with-gbk 
        
        
        Changelog
        =========
        
        
        ========= ====================================================================
        Version   Description
        ========= ====================================================================
        1.10.4    * Fix v1.10.3 adding missing requirements.txt
        1.10.3    * Update pdb service to use v2 API
                  * remove biocarta (website not accesible anymore)
                  * Update Chembl (no API changes)
        1.10.2    * Fix #226 and applied PR from Fix from @GianArauz
                    https://github.com/cokelaer/bioservices/pull/232 about UniProt 
                    error
                  * Update MANIFEST to fix #232
        1.10.1    * allow command line to download genbank and GFF
                  * update pride module to use new PRIDE API (July 2022)
                  * Fixed KEGG bug #225
        1.10.0    * Update uniprot to use the new API (june 2022)
        1.9.0     * Update unichem to reflect new API
        1.8.4     * biomodels. Fix #208
                  * KEGG: fixed #204 #202 and #203
        1.8.3     * Eutils: remove warning due to unreachable URL. Set REST as
                    attribute rather and inheritance. 
                  * NEW biocontainers module
                  * KEGG: add save_pathway method. Fix parsing of structure/pdb entry
                  * remove deprecated function from Reactome
        1.8.2     * Fix suds package in code and requirements
        1.8.1     * Integrated a change made in KEGG service (DEFINITON was changed to
                    ORG_CODE)
                  * for developers: applied black on all modules
                  * switch suds-jurko to new suds community 
        1.8.0     * add main standalone application. 
                  * moved chemspider and clinvitae to the attic
                  * removed picr service, not active anymore
        1.4.X     * NEW RNAseq from EBI in rnaseq_ebi module
                  * 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. 
        1.3.X     * CACHE files are now stored in a general directory in the home
                  * 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     * NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf
        1.1.X     * NEW services: biocarta, pfam, ChEBI, UniChem
        1.0.0:    * first stable release
        0.9.X:    * NEW 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 :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
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
Description-Content-Type: text/x-rst
Provides-Extra: testing
