| Name | parasplit JSON |
| Version |
1.1.3
JSON |
| download |
| home_page | None |
| Summary | An Hi-C tool for cutting sequences using specified enzymes |
| upload_time | 2025-10-27 10:46:52 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | None |
| license | AGPLv3 |
| keywords |
hi-c
hic
bioinformatics
cutsite
|
| VCS |
|
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
<!--
SPDX-FileCopyrightText: 2024 Samir Bertache
SPDX-FileCopyrightText: 2025 2024 Samir Bertache
SPDX-License-Identifier: AGPL-3.0-or-later
SPDX-License-Identifier: CC0-1.0
-->
[]
[]
# PARASPLIT :
## 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:
```bash
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
```bash
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](https://creativecommons.org/licenses/by-nc/4.0/)*
## Dependencies
- pigz
## 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 [samir.bertache.djenadi@gmail.com](mailto:samir.bertache.djenadi@gmail.com).
---
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.
Raw data
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