How to know the number of RAW files for all the public datasets in PRIDE.

[ypriverol]

Recently, someone asked PRIDE support how to get the number of RAW files from all PRIDE projects.

Here, is the best solution:

Before anything, you have to install pridepy:

> pip install --upgrade pridepy

Then download all the file metadata from public datasets in PRIDE:

> pridepy stream-files-metadata -o all_pride_files_metadata.json

This will download a json file named all_pride_files_metadata.json to your local computer with all the file metadata in PRIDE. Then, you can run the following script: https://gist.github.com/ypriverol/f29f59f3b4fd6d7e6fb30ebe2f202c82 and pass as input the downloaded file. It will produce a final output as project_raw_counts.txt with the following lines:

Projects sorted by number of RAW files:
PXD049444: 9100 RAW files
PXD042233: 7444 RAW files
PXD017052: 6763 RAW files
PXD002815: 4311 RAW files
PXD039875: 4019 RAW files
PXD014398: 3987 RAW files
PXD008750: 3936 RAW files
PXD010859: 3748 RAW files
PXD015912: 3206 RAW files
PXD052871: 3140 RAW files
PXD005336: 3071 RAW files
PXD004193: 3053 RAW files
....

Please let us know if this is useful for you.