GTF comparison script

[khajoue2]

Add GTF comparison script for annotation analysis

Description

Added a new Python script that performs comprehensive comparison analysis between two GTF (Gene Transfer Format) files. This tool helps identify structural and content differences between GTF annotations, which is particularly useful when validating changes in annotation pipelines or comparing different versions of genome annotations.

Features

• Detailed comparison of all GTF fields (columns 1-8) with sample differences
• Attribute-level comparison (column 9) with statistics on differences
• Gene-level analysis including:
  • Total gene count comparison
  • Identification of unique genes in each file
  • Special analysis of mitochondrial (MT-) genes
• Generates three detailed report files:
  • *_structural_diff.txt: Analysis of basic GTF structure
  • *_attribute_diff.txt: Detailed attribute differences
  • *_gene_diff.txt: Gene-level comparisons and MT gene analysis

Usage

python3 compare_gtfs.py old.gtf new.gtf --output-prefix comparison_result

Here's a summary of the testing implementation for the GTF comparison script:

Added automated testing framework for GTF file comparison:

1. Created test infrastructure:

   • create_test_gtfs.py: Generates test GTF files with known differences
   • test_gtf_comparison.py: Unit tests to verify comparison functionality
   • GitHub Actions workflow in .github/workflows/gtf_tests.yml

2. Test Coverage:

   • Validates structural differences in GTF fields
   • Checks attribute differences in the 9th field
   • Verifies gene-level comparisons
   • Tests mitochondrial gene handling
   • Confirms proper output file generation

3. CI/CD Integration:

   • Tests automatically run on pushes/PRs affecting build-indices directory
   • Test results uploaded as artifacts in GitHub Actions
   • Working directory configured for 3rd-party-tools/build-indices path

4. How to Run Tests Locally:

python -m unittest test_gtf_comparison.py -v

Files Added:

• test_gtf_comparison.py
• create_test_gtfs.py
• .github/workflows/gtf_tests.yml

Path: /warp-tools/3rd-party-tools/build-indices/

[jessicaway]

This looks great, thanks @khajoue2!