sdrf-pipelines

PyPI version PyPI - Downloads CI Codacy Badge

The official SDRF-Proteomics validator and converter. Validate your sample metadata files and convert them to workflow configurations for OpenMS, MaxQuant, MSstats, and more.

Quick Start with sdrf as a command/line tool

Install python and pipx or just uv

uv:

# Install
uv tool install "sdrf-pipelines[all]"

# Validate your SDRF file
parse_sdrf validate-sdrf --sdrf_file your_file.sdrf.tsv

pipx:

# Install
pipx install "sdrf-pipelines[all]"

# Validate your SDRF file
parse_sdrf validate-sdrf --sdrf_file your_file.sdrf.tsv

That's it! Your SDRF file will be validated against the default mass spectrometry template.

Installation

Installation Command Features
Basic pip install sdrf-pipelines Structural validation + all converters
Full pip install sdrf-pipelines[ontology] + Ontology term validation (EFO, CL, MS, etc.)

The basic installation validates column structure, formatting, and uniqueness. Add [ontology] to also validate that terms exist in their respective ontologies.

Usage

For detailed command documentation, see COMMANDS.md or use the built-in help:

parse_sdrf --help
parse_sdrf validate-sdrf --help

Validation Examples

# Basic validation
parse_sdrf validate-sdrf --sdrf_file sample.sdrf.tsv

# Validate with a specific template
parse_sdrf validate-sdrf --sdrf_file sample.sdrf.tsv --template human

# Skip ontology validation for quick structural checks
parse_sdrf validate-sdrf --sdrf_file sample.sdrf.tsv --skip-ontology

Converter Examples

# Convert to OpenMS format
parse_sdrf convert-openms -s sdrf.tsv

# Convert to MaxQuant format
parse_sdrf convert-maxquant -s sdrf.tsv -f database.fasta -r /path/to/raw/files

# Convert to MSstats annotation
parse_sdrf convert-msstats -s sdrf.tsv -o annotation.csv

# Convert to MHCquant format (samplesheet + search presets)
parse_sdrf convert-mhcquant -s sdrf.tsv -os samplesheet.tsv -op presets.tsv

Development

We use modern Python tooling for development:

Package Manager: uv

We use uv as our package manager for fast, reliable dependency management.

# Install uv (if not already installed)
curl -LsSf https://astral.sh/uv/install.sh | sh

# Create virtual environment and install dependencies
uv sync

# Install with dev dependencies
uv sync --group dev

Code Quality: ruff + pre-commit

We use ruff for linting and formatting, and pre-commit for automated checks.

# Install pre-commit hooks
uv run pre-commit install

# Run all checks manually
uv run pre-commit run --all-files

Running Tests

uv run pytest

For more details, see CONTRIBUTING.md.

Citation

If you use this software, please cite:

Dai C, Füllgrabe A, Pfeuffer J, et al. A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun 12, 5854 (2021). https://doi.org/10.1038/s41467-021-26111-3

For full citation details and BibTeX format, see CITATION.cff.

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for ypriverol from gravatar.com ypriverol

Credits

Author: BigBio Team

License expression

Apache-2.0
View SPDX License List

Requires

Python >=3.10

Provides Extra

all ontology

Tags

multiomics proteomics python sdrf

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

sdrf_pipelines-0.1.6.tar.gz (36.7 MB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

sdrf_pipelines-0.1.6-py3-none-any.whl (602.0 kB view details)

Uploaded Python 3

File details

Details for the file sdrf_pipelines-0.1.6.tar.gz.

File metadata

  • Download URL: sdrf_pipelines-0.1.6.tar.gz
  • Upload date:
  • Size: 36.7 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: uv/0.12.0 {"installer":{"name":"uv","version":"0.12.0","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}

File hashes

Hashes for sdrf_pipelines-0.1.6.tar.gz
Algorithm Hash digest
SHA256 30fb8053e5ee206a40d6d1685204aa9224262d627773c2f9fb7a5cb04a131173
MD5 7bf6dbb74e08694fff0f8d2bbc783232
BLAKE2b-256 5df5f33a35b4e6904d43518c6a0a62a7fbd5c2cb79e93e9388e789d037e08e14

See more details on using hashes here.

File details

Details for the file sdrf_pipelines-0.1.6-py3-none-any.whl.

File metadata

  • Download URL: sdrf_pipelines-0.1.6-py3-none-any.whl
  • Upload date:
  • Size: 602.0 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: uv/0.12.0 {"installer":{"name":"uv","version":"0.12.0","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}

File hashes

Hashes for sdrf_pipelines-0.1.6-py3-none-any.whl
Algorithm Hash digest
SHA256 dfe051f976ad5a07233df84ace8b274245c142ad2bd33965d894581066b6e2bf
MD5 91586795472e32ec2ede5c8d4648da11
BLAKE2b-256 45fb25ac2422483d8b16157ecf530282b4945057719e81e15f8ec9458fa864a9

See more details on using hashes here.

Release history Release notifications | RSS feed

This release

0.1.6 This release

2 files

0.1.5

2 files

0.1.4

2 files

0.1.3

2 files

0.1.2

2 files

0.1.1

2 files

0.1.0

2 files

0.0.33

2 files

0.0.32

2 files

0.0.31

2 files

0.0.30

2 files

0.0.29

2 files

0.0.28

2 files

0.0.27

2 files

0.0.26

2 files

0.0.25

2 files

0.0.24

2 files

0.0.23

2 files

0.0.22

2 files

0.0.21

2 files

0.0.20

2 files

0.0.19

2 files

0.0.18

2 files

0.0.17

2 files

0.0.14

2 files

0.0.13

2 files

0.0.12

2 files

0.0.11

2 files

0.0.10

2 files

0.0.9

2 files

0.0.8

2 files

0.0.7

2 files

0.0.6

2 files

0.0.5

2 files

0.0.4

2 files

0.0.3

2 files

0.0.2

2 files

0.0.1

2 files

Anthropic, PBC Visionary sponsor Bloomberg Visionary sponsor Hudson River Trading Visionary sponsor Meta Visionary sponsor NVIDIA Visionary sponsor Microsoft Sustainability sponsor Depot Continuous Integration AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page