gb-rotate 0.1.4

A command-line utility to rotate and reverse complement GenBank files.

gb_rotate

A basic Python for rotating and reverse complementing GenBank files based on a numerical offset. This tool updates feature annotations to ensure consistency with the transformed sequence. Intended for personal use and originally developed for rotating plastid genomes.

Features

• Rotate GenBank sequences around a specified offset.
• Reverse complement sequences and update annotations accordingly.
• Compatible with GenBank formatting, preserving header and feature details.

Installation

From PyPI

pip install gb_rotate

From repository

1. Clone the repository:

git clone https://github.com/kherronism/gb_rotate.git

2. Build and install locally:

cd gb_rotate
pip install .

Usage

Basic usage

After installation, use the gb_rotate command:

gb_rotate -i <input_file> -o <output_file> -r <rotation_offset> -c

Options

Option	Description
-i, --input-file	Path to the input GenBank file (required).
-o, --output-file	Path to the output GenBank file (required).
-r, --rotation-offset	Rotation offset position (default: 0).
-rc, --reverse-complement	Reverse complement the sequence (optional).

Examples

Rotate only

Rotations should be in the range of 0 to the sequence length. With a rotation_offset of 1000, the first position in the sequence will be the 1001st position in the output.

Rotate a sequence around offset 50000 and save the result:

gb_rotate -i example.gb -o example_rotated.gb -r 50000

Reverse Complement only

Reverse complement a sequence and save the result:

gb_rotate -i example.gb -o example_rc.gb -rc

Combine both

When combining, the reverse complement operation takes place first, followed by the rotation, therefore the offset is applied to the reverse complemented sequence.

Combine both operations:

gb_rotate -i example.gb -o example_modified.gb -r 50000 -rc