JupyterLab Fasta Viewer

A JupyterLab extension for viewing Fasta information. A file renderer for files with .fasta extensions and a mime renderer for the application/vnd.fasta.fasta mimetype is included. This extension uses the MSA Fasta viewer.

To use the file viewer, right-click on a .fasta file and choose the Fasta viewer.

To use the notebook viewer, you can define a Fasta display class like:

from IPython.display import display
class Fasta:
    def __init__(self, data):
        self.data = data
    def _ipython_display_(self):
        bundle = {
            'application/vnd.fasta.fasta': self.data,
            'text/plain': self.data
        }
        display(bundle, raw=True)

and then display Fasta('some fasta data')

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

Prerequisites

• JupyterLab

Installation

Clone this repo into a directory (say jupyterlab-fasta), and then do

jupyter labextension install ./jupyterlab-fasta

Development

For a development install (requires npm version 4 or later), do the following in the repository directory:

npm install
jupyter labextension link .

To rebuild the package and the JupyterLab app:

npm run build
jupyter lab build