pridepy 0.0.16

Python Client library for PRIDE Rest API

pridepy

pridepy is a Python client and CLI for the PRIDE Archive API.

You can:

• download public and private PRIDE files
• download public MassIVE (MSV...), JPOST (JPST...), and iProX (IPX...) datasets directly. MassIVE goes through FTPS at massive-ftp.ucsd.edu, with an automatic HTTPS fallback (via the GNPS2 file index and the massive.ucsd.edu ProteoSAFe endpoint) for networks that block FTP/FTPS; JPOST uses the JSON PROXI endpoint at repository.jpostdb.org for listings and ftp.jpostdb.org for transfers; iProX fetches the dataset's ProteomeXchange XML from download.iprox.org and downloads files over anonymous HTTP
• download by category (RAW, SEARCH, RESULT, etc.)
• stream project and file metadata
• search projects by keyword and filters
• download raw files from ProteomeXchange XML metadata

The downloader supports ftp, aspera, s3, and globus.
By default it starts with FTP, falls back across the remaining protocols when needed, and validates downloaded files (non-empty, and checksum validation when enabled).

Requirements

• Python >=3.9

Installation

Option 1: Install from PyPI with uv (recommended)

Install as a CLI tool:

uv tool install pridepy
pridepy --help

Or run without installing globally:

uvx pridepy --help

Option 2: Install from PyPI with pip

pip install --upgrade pridepy
pridepy --help

Option 3: Install the latest code directly from GitHub

To get features that have not been released to PyPI yet, install straight from a branch. master holds the latest stable code; dev holds the newest (and potentially unstable) development work.

With uv:

# Latest stable (master)
uv tool install "git+https://github.com/PRIDE-Archive/pridepy@master"

# Bleeding edge (dev)
uv tool install "git+https://github.com/PRIDE-Archive/pridepy@dev"

Or with pip:

# Latest stable (master)
pip install --upgrade "git+https://github.com/PRIDE-Archive/pridepy@master"

# Bleeding edge (dev)
pip install --upgrade "git+https://github.com/PRIDE-Archive/pridepy@dev"

You can pin to any branch, tag, or commit by changing the part after @ (e.g. @v0.0.16 or @<commit-sha>).

Option 4: Install from source (development)

git clone https://github.com/PRIDE-Archive/pridepy
cd pridepy
uv sync --extra dev
uv run pridepy --help

Usage

See the usage guide for detailed instructions and examples: downloading data (PRIDE, MassIVE, JPOST, iProX, ProteomeXchange), category and manifest downloads, private files, streaming metadata, searching projects, and the Python API.

pridepy --help

Command	Purpose
download-all-public-raw-files	Download every public RAW file of a dataset
download-all-public-category-files	Download files of one or more categories (RAW, SEARCH, …)
download-file-by-name	Download a single file (public or private)
download-files-by-list	Download a named subset of files from a manifest/CSV
download-files-by-url	Download files from raw http/https/ftp URLs
download-px-raw-files	Download RAW files resolved from a ProteomeXchange accession
list-private-files	List files of a private project (needs credentials)
stream-files-metadata	Stream file metadata (one project or all) to JSON
stream-projects-metadata	Stream all project metadata to JSON
search-projects-by-keywords-and-filters	Search projects by keyword and filters

Quick examples:

# Download all public RAW files of a dataset (any repository)
pridepy download-all-public-raw-files -a PXD008644 -o ./downloads/PXD008644 --checksum-check

# Download a ProteomeXchange dataset by its PXD accession
pridepy download-px-raw-files -a PXD039236 -o ./downloads/PXD039236

# Download a native MassIVE / JPOST / iProX dataset
pridepy download-all-public-raw-files -a MSV000082297 -o ./downloads/MSV000082297

Full option tables and more examples are in docs/usage.md.

Development and Release (uv)

Run tests:

uv run pytest

Lint:

uv run flake8 .

Build distributions:

uv build

pridepy is published via GitHub Actions (.github/workflows/python-publish.yml) using uv build and a PyPI API token secret (PYPI_API_TOKEN).

White Paper

A white paper is available in paper/paper.md.

Contributing

1. Fork the repository
2. Create a branch (git checkout -b feature/my-change)
3. Install dev dependencies (uv sync --extra dev)
4. Run tests and lint (uv run pytest, uv run flake8 .)
5. Commit and push your branch
6. Open a pull request

Citation

Kamatchinathan, S., Hewapathirana, S., Bandla, C., Insua, S., Vizcaíno, J. A., & Perez-Riverol, Y. (2025). pridepy: A Python package to download and search data from PRIDE database. Journal of Open Source Software, 10(107), 7563. doi:10.21105/joss.07563