extract-exons-py

name	extract-exons-py
description	Use when extracting exon coordinates from GTF annotation files for HISAT2 index building or transcriptome analysis.
disable-model-invocation	true
user-invocable	true

extract-exons-py

Quick Start

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

When To Use This Tool

• Extract nonredundant exon intervals from a GTF annotation.
• Prepare exon lists for HISAT2 index building or transcriptome-aware downstream tooling.
• Collapse transcript-specific exon redundancy into a unique coordinate set.

Common Patterns

# 1) Extract exons from a GTF file
extract_exons.py genes.gtf > exons.tsv

# 2) Stream a GTF through stdin
zcat genes.gtf.gz | extract_exons.py - > exons.tsv

# 3) Inspect the first zero-based exon intervals
extract_exons.py genes.gtf | sed -n '1,20p'

Recommended Workflow

1. Obtain a valid GTF annotation file for your reference genome
2. Run extract_exons.py gtf_file to extract exon coordinates (use - for stdin)
3. Add -v flag to print statistics to stderr for validation
4. Use output as input for downstream HISAT2 index building workflows

Guardrails

• Input must be a valid GTF file or - for stdin
• Verify GTF format compatibility before processing large files
• Review stderr output when using verbose mode to validate extraction statistics
• Output coordinates are zero-based (left-1, right-1) and include strand as the fourth column.
• Adjacent exons separated by 5 bp or less are merged before output, so the result is not a raw exon-by-exon dump from the source GTF.
• --help works, but --version is not implemented and exits with an argparse error.