Bioinformatics Command-Line Toolbox

This project is a command-line tool for performing common bioinformatics tasks, including DNA/RNA sequence manipulation and filtering of FASTQ data.

🚀 Features

The script has two main modes of operation:

1. Simple Sequence Processing (process):

   • Accepts one or more sequences as string inputs.
   • Performs one of the following operations:
     • transcribe: Transcribes DNA into RNA (T → U).
     • reverse: Reverses the sequence.
     • complement: Creates the complementary strand.
     • reverse_complement: Creates the reverse-complementary strand.
     • is_palindrome: Checks if a sequence is a palindrome.

2. FASTQ File Filtering (filter):

   • Reads sequences from a FASTQ format file.
   • Filters them based on specified criteria:
     • GC Content: Keeps sequences within a specified GC content range (in percent).
     • Length: Keeps sequences within a specified length range.
     • Quality: Keeps sequences with an average Phred33 quality score above or equal to a given threshold.
   • Saves the filtered sequences in FASTA format.

⚙️ Installation and Project Structure

This script requires Python 3.6+. No external libraries need to be installed. Don't forget to make main.py executable!

Your project should have the following structure for the imports from the modules directory to work correctly:

├── biotools.py # The main executable script ├── modules/ │ ├── init.py # (Can be empty) │ ├── is_nucleic_acid.py │ ├── transcribe.py │ ├── reverse.py │ ├── raw_toolbox.py │ ├── complement_and_reverse.py │ ├── is_palindrome.py │ ├── calculate_quality.py │ └── calculate_gc_content.py └── README.md # This file

All commands are run from the terminal. The basic syntax is:

python main.py [arguments]

Simple Sequence Processing

This project contains toolbox for quick operations on sequence strings:

python main.py [*sequences] [tool]

Tool	Description
transcribe	Transcribes DNA into RNA (replaces T with U)
reverse	Reverses the sequence
complement	Creates the complementary strand
reverse_complement	Creates the reverse-complementary strand
is_palindrome	Checks if the sequence is a palindrome
Examples:

Transcribe a single sequence

python main.py GCTAGTCA transcribe

Get the reverse-complementary strand

python main.py CGTAGTCAGTCGTATGCGTGTATGCATGTGCATTCATCGATGCATTATTACTATCGGA reverse_complement

Check multiple sequences for being a palindrome

python main.py GATATC GAATTC is_palindrome

FASTQ file filtering: coming soon!

Argument	Description	Usage Example
input_file	(Required) Path to the input FASTQ file.	my_reads.fastq
--output_file	(Optional) Path to the output FASTA file. If not provided, the result is printed to the console.	--output_file good.fasta
--gc_bounds	(Optional) GC content range in percent (min max). Default: 0 100. A single value can be passed to set only the upper bound.	--gc_bounds 40 60
--length_bounds	(Optional) Sequence length range (min max). Default: 0 4294967296. A single value can be passed to set only the upper bound.	--length_bounds 100 150
--quality_threshold	(Optional) Minimum average Phred33 quality score. Default: 0.	--quality_threshold 25