hisat2-extract-splice-sites-py

name	hisat2-extract-splice-sites-py
description	Use when extracting splice junctions from GTF annotation files for HISAT2 splice-aware alignment.
disable-model-invocation	true
user-invocable	true

hisat2-extract-splice-sites-py

Quick Start

• Command: hisat2_extract_splice_sites.py [gtf_file]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/hisat2_extract_splice_sites.py
• Reference: references/help.md

When To Use This Tool

• Use hisat2_extract_splice_sites.py when you need known splice junctions from a GTF for splice-aware HISAT2 workflows.
• It is the canonical helper for generating the file consumed by hisat2-build --ss or by aligners via --known-splicesite-infile.
• Use it when you want a minimal extractor focused on splice junction coordinates rather than a general annotation conversion tool.
• It also supports streaming input via -, so it fits compressed or piped annotation workflows.

Common Patterns

# Extract splice junctions from a GTF file
hisat2_extract_splice_sites.py annotation.gtf > splicesites.txt

# Print progress/statistics to stderr
hisat2_extract_splice_sites.py -v annotation.gtf > splicesites.txt

# Stream a compressed GTF via stdin
gzip -cd annotation.gtf.gz | hisat2_extract_splice_sites.py - > splicesites.txt

# Reuse the result during HISAT2 index building
hisat2-build-s genome.fa genome --ss splicesites.txt

Recommended Workflow

1. Obtain a valid GTF annotation file for your reference organism
2. Run hisat2_extract_splice_sites.py annotation.gtf > splice_sites.txt
3. Pass the output file to HISAT2 index building via --ss option
4. Add -v flag if you want diagnostic statistics printed to stderr

Guardrails

• Input must be a valid GTF file or "-" to read from stdin
• Output writes to stdout; redirect to a file to save results
• Use -v only when you want progress/statistics reported to stderr
• This helper does not implement --version; use -h/--help for availability checks