DNA to FASTQ Encoder

Overview

The DNA to FASTQ Encoder provides tool to load binary DNA file and outputs encoded DNA sequence in FASTQ format. The project consists of a Python script (main.py) for command-line usage and a core Python module (dna_to_fastq_encoder.py) that defines the decoding logic.

Requirements

• Python 3.6 or later

Usage

Command Line Interface

To decode a binary-encoded DNA file into FASTQ format and print the output to the standard output, use the main.py script as follows:

python main.py -f path/to/binary/file -l 80

Where:

• -f or --file specifies the path to the binary-encoded DNA file.
• -l or --length specifies the length of the decoded DNA sequence.

As a Module

You can also use the DnaToFastqEncoder class within your Python projects:

from dna_to_fastq_encoder import DnaToFastqEncoder

Encoder = DnaToFastqEncoder(filepath='path/to/binary/file', l=100)
for fastq_str in Encoder.decode_to_fastq():
    print(fastq_str)

Testing

This project includes a testsuite to verify the functionality of the DnaToFastqEncoder class. To run the tests:

1. ensure you have pytest installed
2. set up TEST_FILES_PATH variable in test_dna_to_fastq_encoder.py
3. execute the following command in the project directory:

pytest