leebird/uniprot

Parse utility for UniProt bulk download files

uniprot

Parse utility for UniProt bulk download files

Usage

Generate UniProt AC to Entrez ID mapping

First, downlowd id mapping file (uniprot AC to entrez ID) from UniProt website. URL: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/ File: id_mapping.dat.gz

Then use python extract_ac_to_entrez.py /path/to/id_mapping.dat.gz to generate a pickled file under the same folder.

Generate UniProt json dump

Secondly, download Uniprot dump in XML format from https://www.uniprot.org/downloads (Reviewed (Swiss-Prot)) Use python parser.py /path/to/uniprot_xml_file to generate a json dump of the uniprot data.

parser.py will use the mapping generated in the first step and assume it's under the same folder (look at the end of parser.py for more details)