Utilities Module (chr3d.utils)

Convenience functions and utilities for common chromatin interaction analysis operations.

Overview

The utils module provides:

• Restriction Site Generation: Generate restriction fragment coordinates from genome FASTA
• Loop Conversion: Convert loops to HiGlass-compatible bedpedb format
• Enzyme Detection: Detect restriction enzymes used in Hi-C libraries
• Background Model: Functions for ChIA-PET/HiChIP background modeling

Functions and Classes

Restriction Site Generation

• RestrictionSiteGenerator - Class for generating restriction fragments
• restriction_site_generator - One-call wrapper function

Loop Conversion

• loops_to_beddb - Complete CSV → BEDPE → bedpedb pipeline
• csv_to_bedpe - Convert loops CSV to BEDPE
• bedpe_to_bedpedb - Convert BEDPE to HiGlass bedpedb
• verify_positions - Verify bedpedb coordinates

Enzyme Detection

• detect_restriction_enzyme - Detect restriction enzyme from FASTQ

Background Model

• Background Model Functions - ChIA-PET/HiChIP background modeling

Examples

• Complete Workflow Example - End-to-end pipeline example