pygenomics

PyGenomics performs genomic interval operations and processes high-throughput sequencing data to analyze overlaps, intersections, and unions of genomic regions and to handle read alignments and genomic variants.

Key Features:

• Interval Operations: Computes overlaps, intersections, and unions of genomic regions for interval-based analyses.
• Standard Format Support: Reads and writes BAM, BED, GFF3, and VCF formats for alignments, annotations, and variant data.
• Functional Programming Design: Implements functional programming principles with type annotations to support integration into computational workflows.
• Pure Python Implementation: Implements functionality using only the Python standard library without external dependencies.
• Property-Based Testing: Validates functionality using a property-based testing framework.

Scientific Applications:

• Variant Analysis: Processes and analyzes genomic variants stored in VCF files.
• Annotation Pipelines: Parses and integrates GFF3 annotations into genomic workflows.
• Genomic Data Integration: Incorporates BAM and BED data for read alignment and interval-based studies.

Methodology:

Implements interval-based algorithms in pure Python following a functional programming paradigm with type annotations, parses BAM, BED, GFF3, and VCF formats, and validates behavior using property-based testing.