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bio-genome-intervals-gtf-gff-handling

80 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, and sanitizing malformed files with AGAT. Covers the 1-based-inclusive vs 0-based BED coordinate conversion (start-1 only), deriving implicit features (introns/UTRs/TSS), phase-not-frame, the stop-codon-…

Works with any agent that supports SKILL.md skills.

What this skill can do

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'bio-genome-intervals-gtf-gff-handling' ] || [ -L ~/.agents/skills/'bio-genome-intervals-gtf-gff-handling' ]; then echo 'A skill folder named bio-genome-intervals-gtf-gff-handling already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-genome-intervals-gtf-gff-handling' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-genome-intervals-gtf-gff-handling' ~/.agents/skills/'bio-genome-intervals-gtf-gff-handling' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'bio-genome-intervals-gtf-gff-handling' ~/.claude/skills/'bio-genome-intervals-gtf-gff-handling' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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