@jupyterlab/fasta-extension
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    3.1.1 • Public • Published

    jupyterlab-fasta

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

    demo

    Requirements

    • JupyterLab >= 3.0

    Install

    pip install jupyterlab-fasta

    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.

    Contributing

    Development install

    Note: You will need NodeJS to build the extension package.

    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
    # Change directory to the jupyterlab-fasta directory
    # Install package in development mode
    pip install -e .
    # Link your development version of the extension with JupyterLab
    jupyter labextension develop . --overwrite
    # Rebuild extension Typescript source after making changes
    jlpm run build

    You can watch the source directory and run JupyterLab at the same time in different terminals to watch for changes in the extension's source and automatically rebuild the extension.

    # Watch the source directory in one terminal, automatically rebuilding when needed
    jlpm run watch
    # Run JupyterLab in another terminal
    jupyter lab

    With the watch command running, every saved change will immediately be built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).

    By default, the jlpm run build command generates the source maps for this extension to make it easier to debug using the browser dev tools. To also generate source maps for the JupyterLab core extensions, you can run the following command:

    jupyter lab build --minimize=False

    Uninstall

    pip uninstall jupyterlab-fasta

    Install

    npm i @jupyterlab/fasta-extension

    DownloadsWeekly Downloads

    1,975

    Version

    3.1.1

    License

    BSD-3-Clause

    Unpacked Size

    19 kB

    Total Files

    10

    Last publish

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