Proteomics Data Import

What it does

When your agent uses it

• Tasks that involve Bioinformatics
• Tasks that involve CSV and tabular files

Example prompts

• “/proteomics-data-import”

Requirements

• Python 3

Workflow steps

4 steps, taken from the first numbered list in SKILL.md.

1. 1Load input (--input ) or generate a demo MaxQuant-shaped file (--demo).
2. 2Dispatch to the format-specific importer (proteomics_data_import.py:164-174 _dispatch_import); supported keys are maxquant, fragpipe…
3. 3Rename columns: LFQ intensity → LFQ_ and Intensity → Int_ (proteomics_data_import.py:85); Majority protein IDs → protein_id; Gene names →…
4. 4Write tables/proteins.csv (proteomics_data_import.py:284) + report.md + result.json (:299).

What it can do on your machine

Read from SKILL.md and the folder at commit 6fbd79f. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships script files (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Proteomics Data Import loads about 1.1k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 87 tokens; SKILL.md has 303 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~87

When it runs · the whole SKILL.md, loaded when a task matches

~1.1k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~1.6k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from TianGzlab/OmicsClaw at commit 6fbd79f, republished under its MIT licence (© TianGzlab). 303 words, ~1,133 tokens.

name

proteomics-data-import

description

Load when ingesting a MaxQuant `proteinGroups.txt`, FragPipe `combined_protein.tsv`, DIA-NN report, or generic CSV / TSV protein-quantification table — normalises columns to a standard schema, emits `tables/proteins.csv`. Skip when raw spectra are the input (run the search engine first); the file is already OmicsClaw schema.

version

0.5.0

author

OmicsClaw

license

MIT

emoji

📥

tags

proteomics, import, maxquant, fragpipe, diann, spectronaut

requires

numpy, pandas

<!-- AUTO-GENERATED from skill.yaml (interface) — do not edit by hand. Regenerate: python scripts/generate_skill_md.py <skill_dir> -->

# Demo (synthetic MaxQuant-style)
python omicsclaw.py run proteomics-data-import --demo --output /tmp/import_demo

# Real MaxQuant output
python omicsclaw.py run proteomics-data-import \
  --input proteinGroups.txt --output results/ --format maxquant

# FragPipe combined_protein
python omicsclaw.py run proteomics-data-import \
  --input combined_protein.tsv --output results/ --format fragpipe

# DIA-NN main report
python omicsclaw.py run proteomics-data-import \
  --input report.tsv --output results/ --format diann

# Generic / Spectronaut (rename columns yourself first)
python omicsclaw.py run proteomics-data-import \
  --input my_table.csv --output results/ --format generic

© TianGzlab, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 5 other files (references) in skills/proteomics/proteomics-data-import of TianGzlab/OmicsClaw.

• SKILL.md
• proteomics_data_import.py
• references/methodology.md
• references/output_contract.md
• references/parameters.md
• skill.yaml

Open the folder on GitHubat commit 6fbd79f