diff --git a/README.rst b/README.rst index cbb6446..874d47f 100644 --- a/README.rst +++ b/README.rst @@ -13,11 +13,11 @@ BIOSERVICES: access to biological web services programmatically :target: http://bioservices.readthedocs.org/en/main/?badge=main :alt: Documentation Status -.. image:: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_256.png - :target: https://raw.githubusercontent.com/cokelaer/bioservices/main/doc/_static/bioservices2_256.png +.. 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 3.6, 3.7, 3.8, 3.9 -:Contributions: Please join https://github.com/cokelaer/bioservices and share your notebooks https://github.com/bioservices/notebooks/ +: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 `_ (2013) 29 (24): 3241-3242 @@ -46,7 +46,7 @@ Each contribution has been an encouragement to pursue this project. Thanks to al .. image:: https://contrib.rocks/image?repo=cokelaer/bioservices :target: https://github.com/cokelaer/bioservices/graphs/contributors - + Quick example ============= @@ -56,14 +56,26 @@ 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") + >>> data = u.search("zap70+and+taxonomy_id:9606", frmt="tab", 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") + + Correspondences can be found in:: + + u._legacy_names + + More examples and tutorials are available in the `On-line documentation `_ Current services