qodon (qdn) is a Command Line Genomics tool. Written in C.

It 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 find the installtion instructions at https://github.com/Temi-Tade/qodon

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.

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:

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 |