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Audit Proteomics Exchange (PRIDE) study metadata from the command line.

Quick start

git clone https://github.com/LangeLab/PXAudit.git
cd PXAudit
uv sync
uv run pxaudit check PXD000001

That one command fetches the dataset's metadata and file list, classifies every file, scores it on a FAIR ladder, and writes everything to a local SQLite database.

What you can do with it

• Check a single dataset: pxaudit check PXD000001 scores one accession and prints a summary.
• Audit a whole list: pxaudit bulk-audit --input ids.txt runs through dozens or hundreds of accessions with a progress bar, then exports the results.
• Inspect file inventories: pxaudit manifest PXD000001 lists every file in a dataset with its category, size, and checksum.
• Track over time: every audit writes to the same SQLite database, so you can query tier distributions, spot trends, and flag datasets that need re-scoring after a logic update.
• Work offline: API responses are cached locally. If the network goes down, PXAudit falls back to the cached data with a warning.

How it works

PRIDE API  -->  local cache  -->  file classifier  -->  tier engine  -->  SQLite DB

PXAudit hits two PRIDE REST endpoints per accession (/projects and /files), caches the raw JSON, classifies every filename into one of nine FileClass types, then runs a deterministic Boolean checklist to assign two scores:

• Tier: a 7-level FAIR ladder from None through Diamond
• Quant Tier: a secondary axis from No Quant through Quant-Complete

Results are upserted into three SQLite tables (study, study_files, audit) so nothing gets lost when you re-audit an accession.

Project status

Current release: v0.3.0 (beta). Active development at github.com/LangeLab/PXAudit.