gintervals.import_gff: Import intervals from a GFF/GTF file

In misha: Toolkit for Analysis of Genomic Data

Import intervals from a GFF/GTF file

Description

Reads a GFF3 or GTF file (optionally gzipped) and returns a misha 1D intervals data frame. GFF/GTF are 1-based and inclusive on both ends; coordinates are converted to 0-based half-open by subtracting 1 from start and leaving end as-is.

Usage

gintervals.import_gff(file = NULL, feature = NULL, strand = TRUE, attrs = TRUE)

Arguments

file	path to a GFF/GTF file.
feature	optional feature-type filter (column 3 of GFF). Pass a character vector to keep only those types (e.g. "exon", c("gene", "transcript")).
strand	if TRUE, include the strand column.
attrs	if TRUE, include the raw attributes string as column attrs. The attribute string is not parsed.

Details

Chromosome names are normalized through the active database's CHROM_ALIAS mechanism.

Value

A 1D intervals data frame with columns chrom, start, end, and optionally strand, type, source, score, attrs.

See Also

gintervals.import_bed, gintervals.import_vcf.

misha documentation built on Aug. 24, 2026, 5:14 p.m.