parasplit 1.1.2

An Hi-C tool for cutting sequences using specified enzymes

CUTSITE SCRIPT README

Overview

Parasplit is a Python script designed to process paired-end FASTQ files by fragmenting DNA sequences at specified restriction enzyme sites. It efficiently handles large datasets by leveraging multi-threading for decompression and compression using pigz.

Features

• Find and Utilize Restriction Enzyme Sites: Automatically identifies ligation sites from provided enzyme names and generates regex patterns to locate these sites in sequences.

• Fragmentation: Splits sequences at restriction enzyme sites, creating smaller fragments based on specified seed size.

• Multi-threading: Efficiently processes large datasets by utilizing multiple threads for decompression and compression.

• Custom Modes: Supports different pairing modes for sequence fragments.

Installation

Ensure you have Python 3 installed along with the required dependencies:

sudo apt-get install pigz
pip install parasplit

Usage

The script can be executed from the command line with various arguments to customize its behavior.

Command-Line Arguments

• --source_forward (str): Input file path for forward reads. Default is ../data/R1.fq.gz.

• --source_reverse (str): Input file path for reverse reads. Default is ../data/R2.fq.gz.

• --output_forward (str): Output file path for processed forward reads. Default is ../data/output_forward.fq.gz.

• --output_reverse (str): Output file path for processed reverse reads. Default is ../data/output_reverse.fq.gz.

• --list_enzyme (str): Comma-separated list of restriction enzymes. Default is "No restriction enzyme found."

• --mode (str): Mode of pairing fragments. Options are all or fr. Default is fr.

• --seed_size (int): Minimum length of fragments to keep. Default is 20.

• --num_threads (int): Number of threads to use for processing. Default is 8.

• --borderless: Non conservation of ligations sites

Example Command

parasplit --source_forward="../data/R1.fq.gz" --source_reverse="../data/R2.fq.gz" --output_forward="../data/output_forward.fq.gz" --output_reverse="../data/output_reverse.fq.gz" --list_enzyme=EcoRI,HinfI --mode=all --seed_size=20 --num_threads=8

Main Script

• Pretreatment: Retrieval of restriction sites from the Biopython database and allocation of resources for the different processes.

• Read: Decompression and simultaneous reading of FastQ files. Send reads to a multiprocessing queue

• Frag: Retrieve sequences in a queue. Splits sequences into fragments based on restriction enzyme sites. Create Pairs, and send it in a multiprocessing queue

• WriteAndControl: Stream writing from data from the output queue and compression in parallel

Project architecture

Schéma de l'architecture - Licence : CC BY-NC 4.0

Implementation Details

• The script uses pigz for parallel decompression and compression to handle large datasets efficiently.
• Signal handlers are implemented to ensure graceful termination of processes.
• The main processing function reads input files, processes sequences to identify and fragment them at restriction sites, and writes the results to output files.
• Multi-threading is utilized for various stages of processing, including decompression, fragmentation, and compression.

Dependencies

• Python 3
• pigz

Testing

Documentation of the tests/ Directory

File test_main.py

• Purpose: This file contains unit tests to verify the correct functioning of the tool. The reference files were generated by hicstuff (version 3.2.3) cutsite for a zero seed size and the DpnII enzyme.

• Examples of Tests:

  • test_process_file: Verifies that the cut function correctly processes an input file and generates the expected output file.
  • Additional tests specific to the different functionalities (modes) of the program.

Directory input_data/

• Purpose: Contains specific input data used to test various configurations of your program.
• Examples:
  • R1.fq.gz, R2.fq.gz: Compressed FASTQ files containing DNA sequences for testing fragmentation.

Directory output_data/

• Purpose: Contains the expected results of the tests.
• Examples:
  • output_ref_R1.fq.gz, output_ref_R2.fq.gz: Compressed FASTQ files representing the expected result after processing by your program.

Running Tests

To run the tests, use the following command:

pytest tests/

This command will execute all tests defined in the tests/ directory and ensure that your program functions correctly.

The tree structure of my project :

		├── myproject/
		│   ├── __init__.py
		│   ├── main.py
		│   ├── Frag.py
		│   ├── Read.py
		│   ├── Pretreatment.py
		│   └── WriteAndControl.py
		├── pyproject.toml
		├── requirements-dev.txt
		├── docs/
		│   ├── requirements.txt
		├── test/
		│   ├── __init__.py
		│   ├── test_main.py	
		│   ├── input_data/
		│   │   ├── R1.fq.gz
		│   │   └── R2.fq.gz
		│   └── output_data/
		│       ├── output_ref_R1.fq.gz
		│       ├── output_ref_R2.fq.gz
		│       ├── output_ref_all_R1.fq.gz
		│       └── output_ref_all_R2.fq.gz
		└── README.md

Contact

For questions or issues, please contact [e-mail].

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This README provides an overview of the Cutsite Script's functionality, usage instructions, and implementation details. For more detailed information, refer to the script's source code and docstrings.