| Name | jupyterlab-fasta JSON |
| Version |
3.3.0
JSON |
| download |
| home_page | |
| Summary | Fasta renderer for JupyterLab |
| upload_time | 2023-05-23 12:26:00 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| license | BSD 3-Clause License Copyright (c) 2020-2023, Project Jupyter All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
jupyterlab
traitlets
ipython
pandas
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# jupyterlab-fasta
A JupyterLab extension for rendering
[Fasta](https://en.wikipedia.org/wiki/FASTA_format) data. This extension uses the
[MSA Fasta viewer](http://msa.biojs.net/).
## Requirements
- JupyterLab >= 3.0
## Install
```bash
pip install jupyterlab-fasta
```
## Usage
To render fasta output in IPython:
```python
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](https://yarnpkg.com/) that is installed with JupyterLab. You may use
`yarn` or `npm` in lieu of `jlpm` below.
```bash
# 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.
```bash
# 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:
```bash
jupyter lab build --minimize=False
```
### Uninstall
```bash
pip uninstall jupyterlab-fasta
```
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"description": "# jupyterlab-fasta\n\nA JupyterLab extension for rendering\n[Fasta](https://en.wikipedia.org/wiki/FASTA_format) data. This extension uses the\n[MSA Fasta viewer](http://msa.biojs.net/).\n\n\n\n## Requirements\n\n- JupyterLab >= 3.0\n\n## Install\n\n```bash\npip install jupyterlab-fasta\n```\n\n## Usage\n\nTo render fasta output in IPython:\n\n```python\nfrom IPython.display import display\n\ndef Fasta(data=''):\n bundle = {}\n bundle['application/vnd.fasta.fasta'] = data\n bundle['text/plain'] = data\n display(bundle, raw=True)\n\nFasta(\"\"\">SEQUENCE_1\nMTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG\nLVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK\nIPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL\nMGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL\n>SEQUENCE_2\nSATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI\nATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH\"\"\")\n```\n\nTo render a `.fasta` file, simply open it.\n\n## Contributing\n\n### Development install\n\nNote: You will need NodeJS to build the extension package.\n\nThe `jlpm` command is JupyterLab's pinned version of\n[yarn](https://yarnpkg.com/) that is installed with JupyterLab. You may use\n`yarn` or `npm` in lieu of `jlpm` below.\n\n```bash\n# Clone the repo to your local environment\n# Change directory to the jupyterlab-fasta directory\n# Install package in development mode\npip install -e .\n# Link your development version of the extension with JupyterLab\njupyter labextension develop . --overwrite\n# Rebuild extension Typescript source after making changes\njlpm run build\n```\n\nYou 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.\n\n```bash\n# Watch the source directory in one terminal, automatically rebuilding when needed\njlpm run watch\n# Run JupyterLab in another terminal\njupyter lab\n```\n\nWith 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).\n\nBy 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:\n\n```bash\njupyter lab build --minimize=False\n```\n\n### Uninstall\n\n```bash\npip uninstall jupyterlab-fasta\n```\n",
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