Skill · em Dados, IA e pesquisa

pyopenms

Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when…

Procedência

Antes de instalar

7 arquivos · 68,6 KB · só texto, nenhum script

Instalar na sua CLI

O comando baixa a versão fixada (commit 57f899e) direto da origem, para a pasta que a CLI lê. Precisa de curl (macOS e Linux); no Windows não há comando, porque o Rook Labs é para macOS.

Claude Code

Neste projeto: instala em .claude/skills/pyopenms/.

d=".claude/skills/pyopenms"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pyopenms"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/data_structures.md" "$u/references/data_structures.md" \
  -o "$d/references/feature_detection.md" "$u/references/feature_detection.md" \
  -o "$d/references/file_io.md" "$u/references/file_io.md" \
  -o "$d/references/identification.md" "$u/references/identification.md" \
  -o "$d/references/metabolomics.md" "$u/references/metabolomics.md" \
  -o "$d/references/signal_processing.md" "$u/references/signal_processing.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.claude/skills/pyopenms/.

d="$HOME/.claude/skills/pyopenms"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pyopenms"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/data_structures.md" "$u/references/data_structures.md" \
  -o "$d/references/feature_detection.md" "$u/references/feature_detection.md" \
  -o "$d/references/file_io.md" "$u/references/file_io.md" \
  -o "$d/references/identification.md" "$u/references/identification.md" \
  -o "$d/references/metabolomics.md" "$u/references/metabolomics.md" \
  -o "$d/references/signal_processing.md" "$u/references/signal_processing.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Codex

Neste projeto: instala em .agents/skills/pyopenms/.

d=".agents/skills/pyopenms"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pyopenms"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/data_structures.md" "$u/references/data_structures.md" \
  -o "$d/references/feature_detection.md" "$u/references/feature_detection.md" \
  -o "$d/references/file_io.md" "$u/references/file_io.md" \
  -o "$d/references/identification.md" "$u/references/identification.md" \
  -o "$d/references/metabolomics.md" "$u/references/metabolomics.md" \
  -o "$d/references/signal_processing.md" "$u/references/signal_processing.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.agents/skills/pyopenms/.

d="$HOME/.agents/skills/pyopenms"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pyopenms"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/data_structures.md" "$u/references/data_structures.md" \
  -o "$d/references/feature_detection.md" "$u/references/feature_detection.md" \
  -o "$d/references/file_io.md" "$u/references/file_io.md" \
  -o "$d/references/identification.md" "$u/references/identification.md" \
  -o "$d/references/metabolomics.md" "$u/references/metabolomics.md" \
  -o "$d/references/signal_processing.md" "$u/references/signal_processing.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Antigravity

Neste projeto: instala em .agents/skills/pyopenms/.

d=".agents/skills/pyopenms"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pyopenms"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/data_structures.md" "$u/references/data_structures.md" \
  -o "$d/references/feature_detection.md" "$u/references/feature_detection.md" \
  -o "$d/references/file_io.md" "$u/references/file_io.md" \
  -o "$d/references/identification.md" "$u/references/identification.md" \
  -o "$d/references/metabolomics.md" "$u/references/metabolomics.md" \
  -o "$d/references/signal_processing.md" "$u/references/signal_processing.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Global: instala em ~/.gemini/antigravity-cli/skills/pyopenms/.

d="$HOME/.gemini/antigravity-cli/skills/pyopenms"
u="https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/cli-tool/components/skills/scientific/pyopenms"
curl -fsSL --create-dirs \
  -o "$d/SKILL.md" "$u/SKILL.md" \
  -o "$d/references/data_structures.md" "$u/references/data_structures.md" \
  -o "$d/references/feature_detection.md" "$u/references/feature_detection.md" \
  -o "$d/references/file_io.md" "$u/references/file_io.md" \
  -o "$d/references/identification.md" "$u/references/identification.md" \
  -o "$d/references/metabolomics.md" "$u/references/metabolomics.md" \
  -o "$d/references/signal_processing.md" "$u/references/signal_processing.md" \
  -o "$d/LICENSE" "https://raw.githubusercontent.com/davila7/claude-code-templates/57f899e5394bb8ca166f38eacae8f0853cbfe033/LICENSE"

Peça ao Rook

Já usa o Rook Labs? Cole no chat do Rook: instale a skill https://rooklabs.sh/marketplace/cct.pyopenms

Prévia do SKILL.md

---
name: pyopenms
description: Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working…
---

# PyOpenMS

## Overview

PyOpenMS provides Python bindings to the OpenMS library for computational mass spectrometry, enabling analysis of proteomics and metabolomics data. Use for handling mass spectrometry file formats, processing spectral data, detecting features, identifying peptides/proteins, and performing quantitative analysis.

## Installation

Install using uv:

```bash
uv uv pip install pyopenms
```

Verify installation:

```python
import pyopenms
print(pyopenms.__version__)
```

## Core Capabilities

PyOpenMS organizes functionality into these domains:

### 1. File I/O and Data Formats

Handle mass spectrometry file formats and convert between representations.

**Supported formats**: mzML, mzXML, TraML, mzTab, FASTA, pepXML, protXML, mzIdentML, featureXML, consensusXML, idXML

Basic file reading:

```python
import pyopenms as ms
…

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