A JupyterLab extension for rendering Fasta data. This extension uses the MSA Fasta viewer.
- JupyterLab ^0.30.0
- Node.js >= 5
jupyter labextension install @jupyterlab/fasta-extensionTo 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.
The jlpm command is JupyterLab's pinned version of
yarn that is installed with JupyterLab. You may use
yarn or npm in lieu of jlpm below.
# Clone the repo to your local environment
git clone https://github.com/jupyterlab/jupyter-renderers.git
cd jupyter-renderers
# Install dependencies
jlpm
# Build Typescript source
jlpm build
# Link your development version of the extension with JupyterLab
jupyter labextension link packages/fasta-extension
# Rebuild Typescript source after making changes
jlpm build
# Rebuild JupyterLab after making any changes
jupyter lab buildYou 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 in another terminal tab
jlpm watchjupyter labextension uninstall @jupyterlab/fasta-extension