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bioservices-1.9.0
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Access to Biological Web Services from Python
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bioservices-1.9.0 |
| نام | bioservices |
| نسخه کتابخانه | 1.9.0 |
| نگهدارنده | ['Thomas Cokelaer'] |
| ایمیل نگهدارنده | ['thomas.cokelaer@pasteur.fr'] |
| نویسنده | Thomas Cokelaer |
| ایمیل نویسنده | thomas.cokelaer@pasteur.fr |
| آدرس صفحه اصلی | http://github.com/cokelaer/bioservices |
| آدرس اینترنتی | https://pypi.org/project/bioservices/ |
| مجوز | GPLv3 |
.. 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
#################################################################################
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://anaconda.org/conda-forge/bioservices/badges/version.svg
:target: https://anaconda.org/conda-forge/bioservices
|Codacy-Grade|
: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
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
========= ====================================================================
1.11.2 * Update COG service to be more user-friendly and return all pages
by default
* uniprot set progress to False in the search method
* Merged #250 and #249 user PRs (compress option in uniprot module
and logging issue in biodbnet)
1.11.1 * Fix regression i uniprot.mapping
(https://github.com/cokelaer/bioservices/issues/245)
1.11.0 * Fix uniprot limitation of 25 results only (
* For developers: all services are now refactorised to use services
as an attribute rather than a parent class.
* Remove ReactomeOld and ReactomeAnalysis (deprecated)
* move rnaseq_ebi (deprecated) to attic for book_keeping
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
========= ====================================================================
.. |Codacy-Grade| image:: https://app.codacy.com/project/badge/Grade/9b8355ff642f4de9acd4b270f8d14d10
:target: https://app.codacy.com/gh/cokelaer/bioservices/dashboard
نحوه نصب
نصب پکیج whl bioservices-1.9.0:
pip install bioservices-1.9.0.whl
نصب پکیج tar.gz bioservices-1.9.0:
pip install bioservices-1.9.0.tar.gz