limix/cbgen

Python wrapper around bgen C library.

limix

Genomic analyses require flexible models that can be adapted to the needs of the user.

Limix is a flexible and efficient linear mixed model library with interfaces to Python. It includes methods for

• Single-variant association and interaction testing
• Variance decompostion analysis with linear mixed models
• Association and interaction set tests
• Different utils for statistical analysis, basic i/o, and plotting.

We have an extensive documentation of the library. If you need further help or want to discuss anything related to limix, please, join our forum 💬 and have a chat with us 😃. In case you have found a bug, please, report it creating an issue.

Install

NOTE: We will be maintaining limix 2.0.x for a while, in case you find some missing feature in limix 3.0.x. If that is the case, please, type pip install "limix <3,>=2" in your terminal.

Installation is easy and works on macOS, Linux, and Windows:

pip install limix

If you already have Limix but want to upgrade it to the latest version:

pip install limix --upgrade

Interactive tutorials

• eQTL (requires limix 2.0.x)
• Struct-LMM (requires limix 2.0.x)

Running tests

After installation, you can test it

python -c "import limix; limix.test()"

as long as you have pytest.

Authors

• Christoph Lippert
• Danilo Horta
• Francesco Paolo Casale
• Oliver Stegle

License

This project is licensed under the Apache License License.

cbgen's Issues

pypi is missing Windows builds for cbgen 1.0.2 (1.0.1 is OK)

Let the user specify the probability precision?

Like np.float32 or np.float64.

limix/bgen-reader-py#33

Let the user fetch probabilities only?

limix/bgen-reader-py#33

Python 3.10 wheels

It would be great to have wheels for Python 3.10.

Build macOS arm64 wheels

These were removed at some point (2eacb6d) - it would be good to get them working again.

Add __del__ method to bgen_file

Adding a del method to bgen_file would allow
del cbgen1
to close the file (currently 'with' and '.close()' work, but not del.

pip install on windows complains of missing bgen.dll and python3.dll

I pip installed on a windows machine.
When I tried pytest, it complained:

ImportError while loading conftest 'C:\Users\Carl\AppData\Roaming\Python\Python37\site-packages\cbgen\conftest.py'.
__init__.py:4: in <module>
    from ._bgen_file import bgen_file
_bgen_file.py:11: in <module>
    from ._ffi import ffi, lib
E   ImportError: DLL load failed: The specified module could not be found.

I used https://github.com/lucasg/Dependencies to try to get details of what DLL's couldn't be found. When I loaded _ffi.pyd, the tool reported bgen.dll and python3.dll were missing.

BGEN_CACHE_HOME needs documentation

The BGEN_CACHE_HOME environment variable isn't documented, but is important for folks who need to direct sample files to larger or faster hard drives.

Python 3.11 wheels

It would be very useful to have wheels for Python 3.11

Incompatibility with Anaconda's Python 3.7 on Windows

Anaconda's Python 3.7 for Windows provides

• cffi 1.14.0
• numpy 1.17.0

(See https://docs.anaconda.com/anaconda/packages/py3.7_win-64/)

cbgen and bgen-reader-py require

• numpy>=1.18.1 (bgen-reader-py)
• numpy>=1.17.4 (cbgen)
• cffi>=1.14.2 (cbgen)

Would it be practical to lower the version requirements for cbgen and bgen-reader-py for compatibility with Anaconda?

Implement advance genotype reading

limix/bgen-reader-py#30 (comment)