Giter Club home page Giter Club logo

deeprvat's People

Contributors

bfclarke avatar endast avatar fmunzlin avatar holev avatar marcel-mueck avatar meyerkm avatar

Stargazers

avatar avatar avatar avatar avatar avatar avatar

Watchers

avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar avatar

Forkers

fmunzlin

deeprvat's Issues

Make the preprocessing less UKBB specific

Right now the preprocessing pipeline expects the input vcf files to be in a format which is very specific to how the UKBB data is structured.

We should make this simpler/more general by just specifying a list of vcf files as input. This change also requires changes to how we handle the selection of chromosomes in the preprocessing pipeline.

Deeprvat environment does not support cuda when created using conda

If you create the deeprvat environment using conda pytorch is not installed with CUDA enabled, hence no gpu is used:

(base)  magnus@pc003:~/code/deeprvat (main) 🦖$ conda  env create -f deeprvat_env.yaml  -n conda_deeprvat
...
(base)  magnus@pc003:~/code/deeprvat (main) 🦖$ conda activate conda_deeprvat
(conda_deeprvat) magnus@pc003:~/code/deeprvat (main) 🦖$  python
Python 3.8.17 | packaged by conda-forge | (default, Jun 16 2023, 07:06:00) 
[GCC 11.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
>>> torch.cuda.device_count()
0
>>> print('Current cuda device ', torch.cuda.current_device())
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/data/magnus/mambaforge/envs/conda_deeprvat/lib/python3.8/site-packages/torch/cuda/__init__.py", line 552, in current_device
    _lazy_init()
  File "/data/magnus/mambaforge/envs/conda_deeprvat/lib/python3.8/site-packages/torch/cuda/__init__.py", line 221, in _lazy_init
    raise AssertionError("Torch not compiled with CUDA enabled")
AssertionError: Torch not compiled with CUDA enabled
>>>

When creating it using mamba cuda is enabled.

(base)  magnus@pc003:~/code/deeprvat (main) 🦖$ mamba env create -f deeprvat_env.yaml
...
(conda_deeprvat) magnus@pc003:~/code/deeprvat (main) 🦖$  conda activate deeprvat
(deeprvat) magnus@pc003:~/code/deeprvat (main) 🦖$  python
Python 3.8.17 | packaged by conda-forge | (default, Jun 16 2023, 07:06:00) 
[GCC 11.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torch
>>> torch.cuda.device_count()
2
>>> print('Current cuda device ', torch.cuda.current_device())
Current cuda device  0

Support non-numeric sample names

In preprocess.py, the process_sparse_gt command assumes sample IDs that can be interpreted as integers.

Instead, arbitrary strings as sample IDs should be supported.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.