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Window Subcommand

English | 中文

Usage

gffsub window <input> -i ID [-u N] [-D N] [-a]

Shortcut form (default mode):

gffsub <input> -i ID -u N -D N

-i ID

Target feature ID or gene name. An ID match takes priority; if none matches, gene-name lookup runs next (Name, gene_id, locus_tag, Alias, Dbxref). Required.

-u / -u N / --upstream N

Bases upstream of the feature start. Default 0. Must be a non-negative integer; trailing garbage (e.g. 50abc) is rejected.

-D / -D N / --downstream N

Bases downstream of the feature end. Default 0. Must be a non-negative integer.

-a / -a

  • Plus strand: upstream extends left of start, downstream extends right of end.
  • Minus strand: upstream extends right of end, downstream extends left of start.
  • Without the flag: upstream always left, downstream always right.
  • Window start below 1 is clamped to 1.

Discontinuous features

Multi-line CDS sharing one ID: window covers the full span across all segments.

Example

Sample input (demo.gff3):

##gff-version 3
chr1	src	gene	100	1000	.	+	.	ID=gene01;Name=BRCA1
chr1	src	mRNA	100	1000	.	+	.	ID=tx01;Parent=gene01
chr1	src	exon	100	250	.	+	.	ID=ex01;Parent=tx01
chr1	src	exon	500	750	.	+	.	ID=ex02;Parent=tx01
chr2	src	gene	200	600	.	-	.	ID=gene02

# 200 bp upstream, 500 bp downstream of gene01
# window chr1:1-1500 (start 100-200=-100, clamped to 1; end 1000+500=1500)
./gffsub window demo.gff3 -i gene01 -u 200 -D 500

# strand-aware window for minus-strand gene02
# window chr2:1-800 (downstream 500 left of start: 200-500=-300, clamped to 1; upstream 200 right of end: 600+200=800)
./gffsub window demo.gff3 -i gene02 -u 200 -D 500 -a

# lookup by gene name
./gffsub window demo.gff3 -i BRCA1 -u 1000 -D 1000

# shortcut form in default mode
./gffsub demo.gff3 -i gene01 -u 200 -D 500

Shortcut requires exactly one --id plus any of --up, --down, --strand-aware. No other filter flags are accepted; passing one aborts with an error naming the allowed set.