qodon - a CLI based genomics tool

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qodon (qdn) 🧬

A Command Line Genomics tool. Written in C

qodon (invoked as qdn) is an ultra-fast, lightweight command-line utility for quick genomic sequence manipulations. Written in pure C, it processes sequence arguments natively at bare-metal speeds, making it perfect for rapid testing, scripting, and pipeline integration.

✨ Features

• Zero Overhead: Built in standard C for maximum execution velocity.
• Dual-Mode Engine: Run quick one-off commands from your terminal or drop into a stateful interactive shell context.
• Instant Evaluation: High-performance byte manipulation for zero-lag sequence transformations.
• Core Bio-Utilities: Fast sequence transcription, complementing, reversing, and metric calculations.

🚀 Installation

You can install qodon directly or build from the source code.

1. Direct Install (Linux, x86_64)

Install precompiled binaries by running:

curl -L -o qdn https://github.com/Temi-Tade/qodon/releases/download/v0.2.0/qdn && chmod +x qdn && sudo mv qdn /usr/local/bin/

2. Build from source

Compile qdn natively using any modern C compiler (gcc or clang required):

# Clone the repository
git clone https://github.com/Temi-Tade/qodon.git
cd qodon

# Compile the binary with optimizations
gcc src/main.c -O3 src/lib/qodon.c src/lib/shell.c -o bin/qdn

# Move to your local bin to run it globally
sudo mv qdn /usr/local/bin/

Usage

🐚 Mode 1: Interactive Context Shell

Launch qdn with the -i flag followed by a target sequence to open the interactive context shell. The sequence is loaded directly into the session's workspace memory, allowing you to run rapid back-to-back operations against that specific strand without retyping it.

$ qdn -i ATGCATGC
Entering qodon shell...
Template sequence: ATGCATGC 
Length: 8bps 
GC content: 50.00%
qdn> len
8bps
qdn> cmp
ATGCATGC (Template strand)
||||||||
TACGTACG (Complementary strand)
qdn> gc
50.00%
qdn> rev
ATGCATGC (FWD)
CGTACGTA (REV)
qdn> exit
$

Available Shell Commands

Inside the shell, execute operations directly on the initialized sequence:

Command	Action	Description
cmp	Complement	Generates the complementary DNA/RNA strand
tr	Transcribe	Transcribes DNA to RNA (converts T to U)
rt	Reverse Transcribe	Reverse transcribes RNA to DNA (converts U to T)
rev	Reverse	Reverses the sequence direction
len	Length	Computes the total length of the sequence
gc	GC-Content	Calculates the exact GC content percentage
exit	Exit	Closes the interactive shell session

🛠️ Mode 2: Quick Terminal Flags

For quick one-offs or integration into larger bash scripts, pass an operational flag followed by your target nucleotide sequence string directly to your terminal:

qdn [flag] <SEQUENCE>

Core Flag Operations

Flag	Shell Command	Action	Description
-c	cmp	Complement	Generates the complementary DNA/RNA strand
-t	tr	Transcribe	Transcribes DNA to RNA (converts T to U)
-u	rt	Reverse Transcribe	Reverse transcribes RNA to DNA (converts U to T)
-l	len	Length	Computes the total length of the sequence
-g	gc	GC-Content	Calculates the GC content percentage
-i		Shell Mode	Enter interactive shell

💻 One-off Examples

Get Complementary Strand:

qdn -c ATGC
# Output: TACG

Transcribe DNA to RNA:

qdn -t GATTACA
# Output: CUAAUGU

Reverse Transcribe RNA to DNA

qdn -u UUAGC
# Output: AATCG

Calculate GC Content:

qdn -g CCGGTT
# Output: 66.67%

Get Sequence Length:

qdn -l ATGCATGC
# Output: 8bps

📄 License

This project is licensed under the MIT License.