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FreedomIntelligence/OpenClaw-Medical-SkillsView
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bio-genome-intervals-gtf-gff-handling
Maintainer FreedomIntelligence · Last updated April 1, 2026
Parse and manipulate GTF/GFF annotation files.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-genome-intervals-gtf-gff-handling
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- GTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates.
- df = gtfparse.read_gtf('annotation.gtf').
Source Doc
Excerpt From SKILL.md
Format Comparison
| Feature | GTF | GFF3 |
|---|---|---|
| Coordinate system | 1-based, inclusive | 1-based, inclusive |
| Hierarchy | Implicit (gene_id, transcript_id) | Explicit (Parent attribute) |
| Attribute format | key "value"; | key=value; |
| Comments | # | # |
| Fasta sequences | Not standard | ##FASTA directive |
Filter by feature type
genes = df[df['feature'] == 'gene'] transcripts = df[df['feature'] == 'transcript'] exons = df[df['feature'] == 'exon']
Get specific gene
gene_df = df[df['gene_name'] == 'TP53']
Use cases
- Use bio-genome-intervals-gtf-gff-handling for genomics and bioinformatics workflows.
- Apply bio-genome-intervals-gtf-gff-handling to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- bed-file-basics - BED format and conversion
- interval-arithmetic - Gene/exon overlap analysis
- proximity-operations - TSS proximity analysis
- differential-expression/de-results - Gene coordinate mapping
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