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""")
Clone this repo into a directory (say jupyterlab-fasta), and then do
jupyter labextension install ./jupyterlab-fasta
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