Metadata-Version: 2.1
Name: bioservices
Version: 1.10.1
Summary: Access to Biological Web Services from Python
Home-page: http://github.com/cokelaer/bioservices
Download-URL: http://pypi.python.org/pypi/bioservices
Author: Thomas Cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: Thomas Cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: GPLv3
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
Description-Content-Type: text/x-rst
License-File: LICENSE

#################################################################################
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://raw.githubusercontent.com/cokelaer/bioservices/main/doc/bioservices.png
    :target: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/bioservices.png

:Python_version_available: BioServices is tested for Python 3.6, 3.7, 3.8, 3.9
: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. 

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: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/>`_

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
biocarta              .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biocarta.yml/badge.svg
                         :target: https://github.com/cokelaer/bioservices/actions/workflows/biocarta.yml
biocontainers         .. image:: https://github.com/cokelaer/bioservices/actions/workflows/biocontainersyml/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
========= ====================================================================
1.10.1    * 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
========= ====================================================================





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



