High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
Gtars: Genomic Tools and Algorithms in Rust
Overview
Gtars is a high-performance Rust toolkit for manipulating, analyzing, and processing genomic interval data. It provides specialized tools for overlap detection, coverage analysis, tokenization for machine learning, and reference sequence management.
Use this skill when working with:
Genomic interval files (BED format)
Overlap detection between genomic regions
Coverage track generation (WIG, BigWig)
Genomic ML preprocessing and tokenization
Fragment analysis in single-cell genomics
Reference sequence retrieval and validation
Installation
Python Installation
Install gtars Python bindings:
uv uv pip install gtars
CLI Installation
Install command-line tools (requires Rust/Cargo):
# Install with all features
cargo install gtars-cli --features "uniwig overlaprs igd bbcache scoring fragsplit"# Or install specific features only
cargo install gtars-cli --features "uniwig overlaprs"
Rust Library
Add to Cargo.toml for Rust projects:
[dependencies]gtars = { version = "0.1", features = ["tokenizers", "overlaprs"] }
Core Capabilities
Gtars is organized into specialized modules, each focused on specific genomic analysis tasks:
1. Overlap Detection and IGD Indexing
Efficiently detect overlaps between genomic intervals using the Integrated Genome Database (IGD) data structure.
When to use:
Finding overlapping regulatory elements
Variant annotation
Comparing ChIP-seq peaks
Identifying shared genomic features
Quick example:
import gtars
# Build IGD index and query overlaps
igd = gtars.igd.build_index("regions.bed")
overlaps = igd.query("chr1", 1000, 2000)
See references/overlap.md for comprehensive overlap detection documentation.
2. Coverage Track Generation
Generate coverage tracks from sequencing data with the uniwig module.
from gtars.tokenizers import TreeTokenizer
import gtars
# Step 1: Load training regions
regions = gtars.RegionSet.from_bed("training_peaks.bed")
# Step 2: Create tokenizer
tokenizer = TreeTokenizer.from_bed_file("training_peaks.bed")
# Step 3: Tokenize regions
tokens = [tokenizer.tokenize(r.chromosome, r.start, r.end) for r in regions]
# Step 4: Use tokens in ML pipeline# (integrate with geniml or custom models)
Python vs CLI Usage
Use Python API when:
Integrating with analysis pipelines
Need programmatic control
Working with NumPy/Pandas
Building custom workflows
Use CLI when:
Quick one-off analyses
Shell scripting
Batch processing files
Prototyping workflows
Reference Documentation
Comprehensive module documentation:
references/python-api.md - Complete Python API reference with RegionSet operations, NumPy integration, and data export
references/overlap.md - IGD indexing, overlap detection, and set operations
references/coverage.md - Coverage track generation with uniwig
references/tokenizers.md - Genomic tokenization for ML applications
references/refget.md - Reference sequence management and digests
Gtars serves as the foundation for the geniml Python package, providing core genomic interval operations for machine learning workflows. When working on geniml-related tasks, use gtars for data preprocessing and tokenization.
Performance Characteristics
Native Rust performance: Fast execution with low memory overhead
Parallel processing: Multi-threaded operations for large datasets
Memory efficiency: Streaming and memory-mapped file support
Zero-copy operations: NumPy integration with minimal data copying
Data Formats
Gtars works with standard genomic formats:
BED: Genomic intervals (3-column or extended)
WIG/BigWig: Coverage tracks
FASTA: Reference sequences
Fragment TSV: Single-cell fragment files with barcodes
