vimsa

The VIM-based multiple sequence alignment (MSA) editor.

Installation

Obtain the script file vimsa from this repository, make it executable and put in any of the directories from your $PATH (e.g. /usr/local/bin). E.g.:

sudo curl -o /usr/local/bin/vimsa https://raw.githubusercontent.com/sgtpep/vimsa/master/vimsa
sudo chmod +x /usr/local/bin/vimsa

This script requires VIM or Neovim to be installed and available as vim or nvim in your shell.

Usage

Just open the file in FASTA format:

vimsa /path/file.fasta

vimsa also accepts input from standard input and writes the result to standard output, so it can be used in shell pipes:

cat /path/file.fasta | vimsa
vimsa < /path/file.fasta

To edit a comment to the sequence move the cursor to its line and press gc, edit the text in an opened split view and press ZZ.

The recommended cursor is a non-blinking block. Edit the settings of your terminal and/or your VIM implementation.

Features

• Reads and writes files in FASTA format.
• Reads input in FASTA format from standard input and writes the result to standard output to be used in shell pipes.

Shortcuts

• gC: edit comments of all sequences line by line
• gc: edit a comment of the sequence under cursor

License and Copyright

The project is released under the General Public License (GPL), version 3.

Copyright © 2018, Danil Semelenov, Stas Malavin.