bio-genome-intervals-gtf-gff-handling
Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils. Use when extracting specific features from gene annotations or converting between annotation formats.
npx skills add BioTender-max/awesome-bio-agent-skills --skill gtf-gff-handling --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: bedtools 2.31+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # GTF/GFF Handling **"Parse gene annotations from GTF/GFF"** → Read gene models, extract features by type (gene, exon, CDS), and query attributes from annotation files. - Python: `gffutils.create_db('file.gtf')` (gffutils), `pyranges.read_gtf()` (pyranges) - CLI: `awk` on tab-delimited GTF fields GTF and GFF3 are standard gene annotation formats. Both use 1-based coordinates. ## 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 | ## GTF Forma
- Version Compatibility
- Format Comparison
- GTF Format
- GFF3 Format
- Parse GTF with gtfparse (Python)
- Installation
- Basic Parsing
- Extract Gene Coordinates
- Get Exons for Gene
- Parse GFF with gffutils (Python)
- Create Database
- Query Features
- Get Introns
- Convert Formats with gffread (CLI)
pip install gtfparse pip install gffutils conda install -c bioconda gffread gffread annotation.gtf -o annotation.gff3 gffread annotation.gff3 -T -o annotation.gtf Extract transcript sequences gffread -w transcripts.fa -g genome.fa annotation.gtf Extract CDS sequences gffread -x cds.fa -g genome.fa annotation.gtf Extract protein sequences
What does the bio-genome-intervals-gtf-gff-handling skill do?
Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils. Use when extracting specific features from gene annotations or converting between annotation formats.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill gtf-gff-handling --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.