Use when extracting exon coordinates from GTF annotation files for HISAT2 index building or splice-aware alignment preparation.
hisat2_extract_exons.py [gtf_file]/home/vimalinx/miniforge3/envs/bio/bin/hisat2_extract_exons.pyreferences/help.mdhisat2_extract_exons.py when you need exon coordinates from a GTF to feed into HISAT2 graph/index construction.--exon input consumed by hisat2-build.- can be used to read the GTF from stdin.# Extract exons from a GTF annotation file
hisat2_extract_exons.py annotation.gtf > exons.txt
# Emit progress/statistics to stderr while writing exon coordinates to stdout
hisat2_extract_exons.py -v annotation.gtf > exons.txt
# Stream a compressed GTF through stdin
gzip -cd annotation.gtf.gz | hisat2_extract_exons.py - > exons.txt
# Use the result during HISAT2 index building
hisat2-build-s genome.fa genome --exon exons.txt
hisat2_extract_exons.py annotation.gtf > exons.txt to extract exon coordinates-v flag to print extraction statistics to stderr if needed- as the gtf_file argument to read from stdin rather than shell piping alone-v go to stderr--version; use -h/--help for a quick installation check