Code Monkey home page Code Monkey logo

oakvar-longevity's Introduction

DOI

oakvar-longevity

Oakvar-Longevity is a module of OakVar which annotates user genome with longevity associated gene variants using the longevitymap annotator, and provides longevity PRS, variants, drugs and major risks(oncorisk) reports with longevity-combinedreporter.

The repository contains:

  • postaggregators:

    just_longevitymap - postagregator for longevity report in oakvar

    just_prs - postagregato for polygenic risk scores

    just_cancer and just_coronary- postagregator for major health risks

  • reporters:

    longevity2reporter - outputs prs, longevity report, major risks report (contains cancer and coronary arthery diseases)

  • webviewerwidgets:

    wglongevitymap - widget for presenting a detailed view for longevity annotator

  • other folders for preprocessing information for development purposes

  • environment.yaml file for conda environment

Setting up

First, git clone the repository and activate submodules:

git clone --recurse-submodules [email protected]:dna-seq/oakvar-longevity.git

Then, activate the environment. We provide environment.yaml that allows setting up the project quickly with Conda or Micromamba. Here we describe instructions to install with micromamba, however conda/anaconda installation is the same. You can either do it from bash or with graphical user interface of you IDE. First, install micromamba, then run:

micromamba create --file environment.yaml
micromamba activate oakvar-longevity

After installation OakVar will be available with ov command and you can install the modules with:

ov module install path_to_the_module

Then, you are ready to use. Note: as the project contains submodules if changes happeneed inside any of them you can keep submodules updated with:

git submodule update --recursive --remote

Documentation

You can learn how to install and use modules from this repository from Just-DNA-Seq Documentation

You can join our discord if you want to discuss the project or if you encountered any issue.

oakvar-longevity's People

Contributors

alex-karmazin avatar antonkulaga avatar lady3mlnm avatar marfantyk avatar winternewt avatar

Stargazers

avatar

Forkers

winternewt vovixsw tvk-dev

oakvar-longevity's Issues

longevity combined reporter crashes with

When I run longevitycombined reporter, for example:

ov report -t longevity_combined -d /data/public/results/  /home/public/.oakvar/jobs/default/221008-010214/advocate.vcf.sqlite &>>  reporter.log

I get the following error:

Generating longevity_combined report... 
/usr/lib/python3/dist-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: 1.16.0-unknown is an invalid version and will not be supported in a future release
  warnings.warn(
/usr/lib/python3/dist-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: 1.1build1 is an invalid version and will not be supported in a future release
  warnings.warn(
/usr/lib/python3/dist-packages/pkg_resources/__init__.py:116: PkgResourcesDeprecationWarning: 0.1.43ubuntu1 is an invalid version and will not be supported in a future release
  warnings.warn(
Generating longevity_combined report... 
Traceback (most recent call last):
  File "/usr/local/bin/ov", line 8, in <module>
    sys.exit(main())
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/__main__.py", line 168, in main
    handle_exception(e)
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/__main__.py", line 150, in handle_exception
    raise e
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/__main__.py", line 161, in main
    ret = args.func(args)
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/decorators.py", line 5, in change_args_for_cli
    ret = func(args)
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/cli/report.py", line 1072, in cli_report
    return report(args)
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/decorators.py", line 32, in run_cli_func
    handle_exception(e)
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/__main__.py", line 150, in handle_exception
    raise e
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/decorators.py", line 24, in run_cli_func
    ret = func(args)
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/cli/report.py", line 1176, in report
    handle_exception(e)
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/__main__.py", line 150, in handle_exception
    raise e
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/cli/report.py", line 1166, in report
    response_t = loop.run_until_complete(reporter.run())
  File "/data/public/.local/lib/python3.10/site-packages/nest_asyncio.py", line 90, in run_until_complete
    return f.result()
  File "/usr/lib/python3.10/asyncio/futures.py", line 201, in result
    raise self._exception.with_traceback(self._exception_tb)
  File "/usr/lib/python3.10/asyncio/tasks.py", line 232, in __step
    result = coro.send(None)
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/cli/report.py", line 428, in run
    raise e
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/cli/report.py", line 416, in run
    await self.write_data(level, pagesize=pagesize, page=page, make_filtered_table=make_filtered_table, add_summary=add_summary)
  File "/data/public/.local/lib/python3.10/site-packages/oakvar/cli/report.py", line 445, in write_data
    self.write_header(level)
  File "/home/public/.oakvar/modules/reporters/longevity_combinedreporter/longevity_combinedreporter.py", line 117, in write_header
    self.columns = self.col_info(level)
  File "/home/public/.oakvar/modules/reporters/longevity_combinedreporter/longevity_combinedreporter.py", line 51, in col_info
    module['start'] = module['lastcol'] - module['count']
KeyError: 'lastcol'

utility scripts have hard-coded pathes

Some of the utility scripts have hard-coded pathes like "'C:/dev/opencravat_longevity/annotators/longevitymap/data/longevitymap.csv'", if you want them to be usable, maybe the path can be given as parameter of the CLI ?

add type-hints

I see that most of the code does not contain type-hints that harms readability, please, do not be lazy and add them at least to functions

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.