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.py
to not have the-dev
suffix - Packages the code in both a tar archive and a wheel using
build
- Uploads to PyPI using
twine
. Be sure to have a.pypirc
file 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 minor
after.
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