DIA-Aspire-rescore

A rescoring module for DIA-Aspire.

• Github repository: https://github.com/5h4ng/DIA-Aspire-rescore/

Installation

Install directly from GitHub using pip:

pip install git+https://github.com/5h4ng/DIA-Aspire-rescore.git

Quick Start

Generate Rescoring Features

Generate comprehensive features for rescoring DIA-NN identifications:

dia-aspire-rescore generate-features \
    --report path/to/diann_report.parquet \
    --ms-file-dir path/to/ms_files/ \
    --ms-file-type mzml \
    --output-dir ./output

Chromatogram Extraction

Extract ion chromatograms based on the spectral library:

dia-aspire-rescore extract-xic \
    --report path/to/diann_report.parquet \
    --speclib path/to/speclib.tsv \
    --ms-file-dir path/to/ms_files/ \
    --ms-file-type mzml \
    --output-dir ./output/xic

For Developers

Requirements

• Python 3.9–3.13
• Git
• uv

Setup

git clone https://github.com/5h4ng/DIA-Aspire-rescore.git
cd DIA-Aspire-rescore
uv sync

Common Commands

# Lint / format
make check
# Tests
make test

TODO

• Generate rescore engine compatible output (PIN file format)
• Integrate mokapot as built-in rescore engine
• Feature refinement and expansion

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Repository initiated with fpgmaas/cookiecutter-uv.