expression-filtering.md

Expression Filtering

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Syntax

-I 'FIELD OP VALUE'   # keep matching records
-E 'FIELD OP VALUE'   # drop matching records

Multiple -I and -E flags combine with AND logic. Within one expression: && (and), || (or), ! (not), ().

Quote values with spaces or special characters using double quotes.

Operators

Operator	Meaning
==	string equal
!=	string not equal
~	regex match
!~	regex not match
<	numeric less than
<=	numeric less or equal
>	numeric greater than
>=	numeric greater or equal

Logic examples

-I 'length >= 100 && strand == "+"'
-I 'type == "gene" || type == "mRNA"'
-I '!(type == "gene")'

Built-in fields

Field	Source
seqid	column 1
source	column 2
type	column 3
start	column 4
end	column 5
length	end - start + 1
score	column 6
strand	column 7
phase	column 8
attrs	column 9 (raw)

Attribute fields

Field	GFF3 key
ID	ID
Name	Name
Parent	Parent
Alias	Alias
Dbxref	Dbxref
Note	Note
biotype	biotype
gene_id	gene_id
transcript_id	transcript_id
locus_tag	locus_tag
attr.KEY	any column-9 attribute

GTF input: gene_id / transcript_id resolve from record fields. Other attributes use the attr. prefix.

Numeric comparison

start, end, length, and score are numeric for <, <=, >, >=, ==, !=.

Missing attributes

• ==, ~, <, <=, >, >= do not match (record excluded by -I).
• != and !~ match (record kept by -I).

Examples

gffsub ann.gff3 -t exon -I 'length >= 100'
gffsub ann.gff3 -E 'length < 10'
gffsub ann.gff3 -t exon -I 'length >= 200 && strand == "+"'