bioshell-cli 0.2.0

A CLI tool for running various Bioinformatics Python scripts.

BioShell CLI

BioShell is a simple command-line interface (CLI) tool designed to help you run and execute various BioPython-based bioinformatics scripts interactively.

Installation

You can install the package directly from PyPI:

pip install bioshell-cli

Usage

Once installed, you can start the interactive menu by simply running:

bioshell

This will present a menu of 10 pre-configured bioinformatics programs:

1. Sequence operations (slice, concatenate, transcribe, translate)
2. Reading FASTA files
3. Creating and writing GenBank files
4. Converting FASTA to GenBank
5. Managing sequence features and annotations
6. Fetching data from NCBI Entrez
7. Pairwise sequence alignment
8. Multiple sequence alignment using MUSCLE
9. Phylogenetic tree construction (UPGMA)
10. PDB structure visualization in 3D

Simply select the number of the script you want to run!