GUI to visualize and process variant data
cutevariant is a light standalone viewer of genetic variation written in Python for Qt. It allows you to view and filter VCF and other format files.
pip install cutevariant # install cutevariant # run
Installation on Windows
Pyside2 is not currently (2019 May) functional on Cygwin, so Cutevariant will not work on Cygwin.
- Install Python3.6+
- Install like the previous chapter said.
- Add the path of python scripts executables to your PATH variable; Something like:
Two executables are generated in this directory:
- cutevariant_win_dbg.exe: Open a console in background to see debugging messages. Note: Qt libs seems to have a very high loglevel and such a verbosity could make the program unusable. - cutevariant.exe: Standard executable.
Developement in progress
Complete rewriting from Cpp to Python.
To get tests running
git clone email@example.com:labsquare/cutevariant.git cd cutevariant virtualenv -p /usr/bin/python3 venv source ven/bin/activate make install_deps # install make run # start application make test # start tests
Development & release cycle
Use zest.releaser to handle the version and distribution through pypi.
pip install zest.releaser[recommended]
To yield a new release, use:
Development on Windows (good luck)
Install make (optional)
pip install wheel git clone https://github.com/ysard/cutevariant.git git fetch git checkout dev # or devel make install # or pip install --user -e .[dev]
Executable files are located here:
- Executable path: C:\Users<username>\AppData\Roaming\Python\Python37\Scripts\cutevariant.exe
Build standalone program/archive/blob[add synonyms here] on Windows using cx_freeze
Strongly discouraged: You will generate an archive of 350Mo just for a program of less than 900Ko (including 550Ko of fonts and icons).
pip install cx_freeze
Build a blob:
Your blob is in
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