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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

Project Purpose

Agentomics is a collection of standalone CLI tools built with pyopenms for proteomics and metabolomics workflows. These tools fill gaps not yet covered by OpenMS/pyopenms. All code in this repo is agentic-only development — written entirely by AI agents.

Commands

# Install dependencies for a specific tool
pip install -r tools/proteomics/peptide_analysis/peptide_mass_calculator/requirements.txt

# Lint a specific tool
ruff check tools/proteomics/peptide_analysis/peptide_mass_calculator/

# Run tests for a specific tool
PYTHONPATH=tools/proteomics/peptide_analysis/peptide_mass_calculator python -m pytest tools/proteomics/peptide_analysis/peptide_mass_calculator/tests/ -v

# Lint all tools
ruff check tools/

# Run all tests across all tools
for d in tools/*/*/*/; do PYTHONPATH="$d" python -m pytest "$d/tests/" -v; done

# Run a script directly
python tools/proteomics/peptide_analysis/peptide_mass_calculator/peptide_mass_calculator.py --sequence PEPTIDEK --charge 2
python tools/metabolomics/spectral_analysis/isotope_pattern_matcher/isotope_pattern_matcher.py --formula C6H12O6

Architecture

Per-Tool Directory Structure

Each tool is a self-contained directory under tools/<domain>/<topic>/<tool_name>/:

tools/<domain>/<topic>/<tool_name>/
├── <tool_name>.py        # The tool (importable functions + click CLI)
├── requirements.txt      # pyopenms + script-specific deps
├── README.md             # Usage examples
└── tests/
    ├── conftest.py       # requires_pyopenms marker + sys.path setup
    └── test_<tool_name>.py

Domains: proteomics/, metabolomics/

Proteomics topics: spectrum_analysis/, peptide_analysis/, protein_analysis/, fasta_utils/, file_conversion/, quality_control/, targeted_proteomics/, identification/, ptm_analysis/, structural_proteomics/, specialized/, rna/, signal_processing/, map_alignment/, quantification/, inference/, dia_analysis/

Metabolomics topics: formula_tools/, feature_processing/, spectral_analysis/, compound_annotation/, drug_metabolism/, isotope_labeling/, lipidomics/, export/, identification/, preprocessing/

Key Patterns

  • pyopenms import wrapped in try/except with user-friendly error message
  • Mass-to-charge: (mass + charge * PROTON) / charge with PROTON = 1.007276
  • Every script has dual interface: importable functions + click CLI + __main__ guard
  • Tests use @requires_pyopenms skip marker from conftest.py
  • File-I/O scripts use synthetic test data generated with pyopenms objects

Contributing

See AGENTS.md for the full AI contributor guide. Two Claude Code skills are available:

  • contribute-script — guided workflow for adding a new script
  • validate-script — validate any script in an isolated venv (ruff + pytest)