gffsub

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Subset GFF3 and GTF annotation files by region, feature ID, attribute, or gene model. Pick longest isoforms, switch formats, write summaries.

Getting Started

git clone https://github.com/WWz33/gffsub.git
cd gffsub && make -j

Minimal GFF3:

printf '%s\n' '##gff-version 3' \
  $'chr1\t.\tgene\t1\t100\t.\t+\t.\tID=GeneA;Name=GeneA' \
  $'chr1\t.\tmRNA\t1\t100\t.\t+\t.\tID=mRNA1;Parent=GeneA' \
  $'chr1\t.\texon\t1\t100\t.\t+\t.\tID=exon1;Parent=mRNA1' > data/smoke.gff3

./gffsub data/smoke.gff3 -r chr1:1-100 -t gene
./gffsub data/smoke.gff3 -i GeneA -C

Usage

gffsub <input.gff3> [options]
gffsub query|window <input.gff3> [options]

See ./gffsub -h for the full flag list.

Common options

Flag	Default	Description
-r, --region	—	1-based inclusive CHR:START-END
-b, --bed	—	BED intervals (0-based half-open)
-i, --id / --ids	—	exact feature ID(s)
-n, --name	—	gene by common naming keys
-w, --where KEY=VALUE	—	exact column-9 attribute
-C, --children	off	include descendants of selector hits
-p, --parents	off	include ancestors
-m, --model	off	full gene model
-N, --nearest REGION	—	nearest gene on same seqid
-u, --up / -D, --down	0	window (bp) around -i
-a, --strand-aware	off	window follows feature strand
-t, --type	—	type column filter; comma list, ^LIST excludes; repeatable
-L, --longest	off	one transcript/gene: CDS length if any CDS, else exon
--longest-type	auto	isoform type for -L; auto-detects transcript class
-@, --threads	1	threads for -L
--format	gff3	gff3|gtf|gtf2|gtf3|bed
-o, --output	stdout	output file
-s, --summary	off	TSV stats by seqid × type (like seqkit stats)
-S, --seqid	—	keep seqids; ^LIST excludes

Input / Output

Kind	Notes
Annotation	GFF3/GTF-style feature records
GFF/GTF / -r	1-based inclusive
BED	0-based half-open

Documentation

Full guides in docs/:

• Getting Started
• Region and BED Filtering
• Feature ID and Gene Name Lookup
• Gene Model Expansion
• Attribute Filtering
• Expression Filtering
• Longest Isoform Selection
• Window Subcommand
• Output Formats
• Summary Output
• GTF Input Handling
• Library API

License

MIT License