extract-splice-sites-py

name	extract-splice-sites-py
description	Use when extracting splice junction sites from GTF annotation files for HISAT2 genome indexing or RNA-seq alignment workflows.
disable-model-invocation	true
user-invocable	true

extract-splice-sites-py

Quick Start

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

When To Use This Tool

• Extract unique splice junction coordinates from a GTF annotation.
• Prepare splice-site lists for HISAT2 index building and splice-aware alignment workflows.
• Summarize transcript exon structures into one junction set per genome annotation.

Common Patterns

# 1) Extract splice junctions from a GTF file
extract_splice_sites.py genes.gtf > splice_sites.tsv

# 2) Stream a compressed GTF through stdin
zcat genes.gtf.gz | extract_splice_sites.py - > splice_sites.tsv

# 3) Emit junctions and summary statistics together
extract_splice_sites.py -v genes.gtf > splice_sites.tsv

Recommended Workflow

1. Prepare a valid GTF annotation file for your reference genome.
2. Run extract_splice_sites.py [gtf_file] to extract splice sites (use - to read from stdin).
3. Add -v flag if you want statistics printed to stderr.
4. Use output as input for HISAT2 index building.

Guardrails

• Input must be a GTF file; other formats are not supported.
• Use - as the gtf_file argument when piping via stdin.
• No --version flag available; check installation via bioconda/hisat2 package.
• Output coordinates are zero-based donor/acceptor boundaries (left-1, right-1) plus strand.
• Exons separated by 5 bp or less are merged before junction extraction, so tiny gaps do not become splice sites.
• With -v, the script prints transcript/exon/intron summary statistics to stderr while still writing splice sites to stdout.