FASTX IO Wrapper

A flexible FastxIOWrapper API for reading and writing FASTA/FASTQ (including gzip/bgzip-compressed files) seamlessly.

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🧬 Overview

This project provides two main components:

1. fastx_io_wrapper.py

A high-level wrapper for FASTA/FASTQ file I/O supporting:

• Automatic format inference (.fa, .fq, .gz, etc.);
• Context-managed read/write operations;
• Support for single-end and paired-end datasets;
• Quality score simulation utilities (QualitySimulator).

Provides:

• FastxIOWrapper: unified I/O for FASTA/FASTQ (+gzip/bgzip)
• PairedFastxIOWrapper: coordinated read/write for paired-end data
• QualitySimulator: generates mock PHRED quality scores and quality strings
• Helper functions for inferring format, trimming, pairing, and converting

2. fasta_splitter.py

A command-line tool and API for:

• Splitting large FASTA sequences into smaller windows (by size or coverage);
• Generating paired-end reads with configurable gaps or overlaps;
• Simulating FASTQ quality scores for downstream testing;
• Writing FASTA or FASTQ output, including compressed files.

FASTA_Splitter.py

Implements:

• Sequence window splitting by size or coverage;
• Paired-end read generation with optional overlaps;
• Integration with FastxIOWrapper and QualitySimulator;
• Command-line interface (CLI) for batch operations.
• Handles .fa, .fasta, .fq, .fastq, .gz, .bgz automatically.
• Detects format from file extension or input stream content.

🚀 Command-Line Usage

python3 fasta_splitter.py \
  -i genome.fa \
  -w 150 \
  -c 1.0 \
  -p read1.fq.gz read2.fq.gz \
  -g 0

Splits genome.fa into 150-bp reads in paired-end format, achieving roughly 1× coverage, outputting to read1.fq.gz and read2.fq.gz in a compressed format (BGZIP), with fixed qualities.

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🧩 Dependencies

• biopython
• tqdm