daichengxin / pridepy

Python client for PRIDE Archive Rest API.

pridepy: Python client for PRIDE Archive database

Python Client library for PRIDE Rest API

Installation

To install, simply use pip:

$ pip install --upgrade pridepy

Examples

Download all the raw files from a dataset(eg: PXD012353). Warning: Raw files are generally large in size, so it may take some time to download depending on the number of files and file sizes.

$ pridepy download-all-raw-files -a PXD012353 -o /Users/yourname/Downloads/foldername/

Download single file by name

$ pridepy download-files-by-name -a PXD022105 -o /Users/yourname/Downloads/foldername/ -f checksum.txt

Search projects with keywords and filters

$ pridepy search-projects-by-keywords-and-filters --keyword accession:PXD012353

Search files with filters

$ pridepy get-files-by-filter --filter fileCategory.value==RAW

Search protein-evidences with keywords and filters

$ pridepy search-protein-evidences --project_accession PXD012353

Search spectra-evidences with keywords and filters

$ pridepy search-spectra-evidences --usi "mzspec:PXD019317:sh_5282_HYK_101018_Mac_D_25mM.mzML:scan:10138:YAAMVTC[UNIMOD:4]MDEAVRNITWALKR/3"

Use below command to view list of commands available

$ python3 pridepy.py --help

  download-all-raw-files          
  download-files-by-name          
  get-files-by-filter             
  get-files-by-project-accession  
  get-projects                    
  get-projects-by-accession       
  get-reanalysis-projects-by-accession
  get-similar-projects-by-accession
  search-peptide-evidences        
  search-projects-by-keywords-and-filters
  search-protein-evidences       
  search-spectra-evidences        
  update-metadata                 

NOTE

Please make sure you are using Python3, not Python 2.7 version.

Citation

Selvakumar Kamatchinathan, Suresh Hewapathirana, Yasset Perez-Riverol. (2021, January 28). pridepy: python client for the PRIDE Archive database (Version v0.0.2).