hisat2-extract-exons-py

name	hisat2-extract-exons-py
description	Use when extracting exon coordinates from GTF annotation files for HISAT2 index building or splice-aware alignment preparation.
disable-model-invocation	true
user-invocable	true

hisat2-extract-exons-py

Quick Start

• Command: hisat2_extract_exons.py [gtf_file]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2_extract_exons.py
• Full reference: See references/help.md

When To Use This Tool

• Use hisat2_extract_exons.py when you need exon coordinates from a GTF to feed into HISAT2 graph/index construction.
• It is the appropriate companion script for generating the --exon input consumed by hisat2-build.
• Use it when your annotation source is GTF and you want a lightweight extractor rather than a general-purpose annotation parser.
• It also works in streaming workflows because - can be used to read the GTF from stdin.

Common Patterns

# 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

Recommended Workflow

1. Prepare or obtain a valid GTF annotation file for your reference genome
2. Run hisat2_extract_exons.py annotation.gtf > exons.txt to extract exon coordinates
3. Add the -v flag to print extraction statistics to stderr if needed
4. Use the output file in downstream HISAT2 index building or alignment steps

Guardrails

• Input must be a valid GTF file; other annotation formats are not supported
• Use - as the gtf_file argument to read from stdin rather than shell piping alone
• Redirect stdout explicitly to save output; statistics with -v go to stderr
• This helper does not implement --version; use -h/--help for a quick installation check