jupyterlab/jupyterlab-fasta

Name: jupyterlab-fasta

Owner: The Jupyter Attic

Owner: JupyterLab

Description: A JupyterLab Fasta viewer

Created: 2017-07-13 16:23:38.0

Updated: 2018-01-17 17:54:10.0

Pushed: 2017-10-25 12:35:29.0

Homepage:

Size: 620

Language: TypeScript

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README

This repo is deprecated. The Fasta viewer has been moved to https://github.com/jupyterlab/jupyter-renderers

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:

 IPython.display import display
s 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')

a(""">SEQUENCE_1
TAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
KVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
ASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
YVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
UENCE_2
SEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH""")

Prerequisites

• JupyterLab

Installation

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

ter labextension install ./jupyterlab-fasta

Development

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

install
ter labextension link .

To rebuild the package and the JupyterLab app:

run build
ter lab build