Python Client library for PRIDE Rest API
Project description
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.
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