fasta-extension

fasta-extension

A JupyterLab extension for rendering Fasta data. This extension uses the MSA Fasta viewer.

Prerequisites

• JupyterLab ^0.27.0

Usage

To render fasta output in IPython:

from IPython.display import display

def Fasta(data=''):
    bundle = {}
    bundle['application/vnd.fasta.fasta'] = data
    bundle['text/plain'] = data
    display(bundle, raw=True)    

Fasta(""">SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH""")

To render a .fasta file, simply open it:

Install

jupyter labextension install @jupyterlab/fasta-extension

Development

# Clone the repo to your local environment
git clone https://github.com/jupyterlab/jupyter-renderers.git
cd jupyter-renderers
# Install dependencies
npm install
# Build Typescript source
npm run build
# Link your development version of the extension with JupyterLab
jupyter labextension link packages/fasta-extension
# Rebuild Typescript source after making changes
npm run build
# Rebuild JupyterLab after making any changes
jupyter lab build

You can watch the jupyter-renderers directory and run JupyterLab in watch mode to watch for changes in the extension's source and automatically rebuild the extension and application.

# Run jupyterlab in watch mode in one terminal tab
jupyter lab --watch
# Watch the jupyter-renderers directory
npm run watch

Uninstall

jupyter labextension uninstall @jupyterlab/fasta-extension