pybedtools.bedtool.BedTool.introns

BedTool.introns(gene: str = 'gene', exon: str = 'exon') → BedTool

Create intron features (requires specific input format).

NOTE: this method assumes a simple file with non-overlapping exons. For more sophisticated features, consider the gffutils package instead.

Given a BED12 or a GFF with exons, create a new BedTool with just introns. The output is a bed6 file with the score column (5) being one of ‘intron’/’utr5’/’utr3’