Generate karyotype pictures using Ideogram.js.
Project description
pydeogram
Generate karyotype pictures using Ideogram.js.
💪 Getting Started
pydeogram helps you make karyotype plots for your gene lists using
Ideogram.js.
import pydeogram
symbols = ["ARFGEF1", "ARFGEF2", "ARFGEF3"]
pydeogram.to_html_path(symbols, path="~/Desktop/argef_ideogram.html")
This also works in a Jupyter notebook. Note you need to run the
prepare_jupyter and to_jupyter functions in succession. I'm looking
for a fix for this so it can be in a single function, but Javascript is
hard.
The pydeogram has a CLI that can do the same thing:
$ pydeogram write ARFGEF1 ARFGEF2 ARFGEF3 -o ~/Desktop/argef_ideogram.html
🚀 Installation
The most recent release can be installed from PyPI with:
$ pip install pydeogram
The most recent code and data can be installed directly from GitHub with:
$ pip install git+https://github.com/cthoyt/pydeogram.git
👐 Contributing
Contributions, whether filing an issue, making a pull request, or forking, are appreciated. See CONTRIBUTING.md for more information on getting involved.
👋 Attribution
⚖️ License
The code in this package is licensed under the MIT License.
🍪 Cookiecutter
This package was created with @audreyfeldroy's cookiecutter package using @cthoyt's cookiecutter-snekpack template.
🛠️ For Developers
See developer instructions
The final section of the README is for if you want to get involved by making a code contribution.
Development Installation
To install in development mode, use the following:
$ git clone git+https://github.com/cthoyt/pydeogram.git
$ cd pydeogram
$ pip install -e .
🥼 Testing
After cloning the repository and installing tox with pip install tox, the unit tests in the tests/ folder can be
run reproducibly with:
$ tox
Additionally, these tests are automatically re-run with each commit in a GitHub Action.
📖 Building the Documentation
The documentation can be built locally using the following:
$ git clone git+https://github.com/cthoyt/pydeogram.git
$ cd pydeogram
$ tox -e docs
$ open docs/build/html/index.html
The documentation automatically installs the package as well as the docs
extra specified in the setup.cfg. sphinx plugins
like texext can be added there. Additionally, they need to be added to the
extensions list in docs/source/conf.py.
📦 Making a Release
After installing the package in development mode and installing
tox with pip install tox, the commands for making a new release are contained within the finish environment
in tox.ini. Run the following from the shell:
$ tox -e finish
This script does the following:
- Uses Bump2Version to switch the version number in the
setup.cfg,src/pydeogram/version.py, anddocs/source/conf.pyto not have the-devsuffix - Packages the code in both a tar archive and a wheel using
build - Uploads to PyPI using
twine. Be sure to have a.pypircfile configured to avoid the need for manual input at this step - Push to GitHub. You'll need to make a release going with the commit where the version was bumped.
- Bump the version to the next patch. If you made big changes and want to bump the version by minor, you can
use
tox -e bumpversion minorafter.
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