genipe | Genome-wide imputation pipeline | Genomics library

by pgxcentre Python Version: 1.5.0 License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | genipe Summary

genipe is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. genipe has no bugs, it has no vulnerabilities, it has build file available and it has low support. However genipe has a Non-SPDX License. You can install using 'pip install genipe' or download it from GitHub, PyPI.

Genome-wide imputation pipeline

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Quality

Security

License

Reuse

Support

genipe has a low active ecosystem.

It has 25 star(s) with 7 fork(s). There are 8 watchers for this library.

It had no major release in the last 12 months.

There are 6 open issues and 49 have been closed. On average issues are closed in 90 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of genipe is 1.5.0

Quality

genipe has 0 bugs and 0 code smells.

Security

genipe has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

genipe code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

genipe has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

genipe releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

genipe saves you 5552 person hours of effort in developing the same functionality from scratch.

It has 11635 lines of code, 344 functions and 36 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

Top functions reviewed by kandi - BETA

kandi has reviewed genipe and discovered the below as its top functions. This is intended to give you an instant insight into genipe implemented functionality, and help decide if they suit your requirements.

Find exclusion before phasing
Get the chromosome encoding
Checks if a given chromosome is reverse
Parse an impute2 file
Generate R script
Parse a line from a single line
Check the arguments for IMPUTE2
Return True if fn is a file - like object
Get the file prefix
Exclude markers before phasing
Launch tasks
Extract markers
Creates the argument parser
Get the chromosome length for each chromosome
Runs the shapeit command
Gathers the execution time for each chromosome
Phase marker markers
Gather the cross - validation statistics
Merge IMPUTE2 files
Gathers information about a specific map file
Impute markers from required chromosomes
Compute the phenotypes
Execute the drmaa command
Gather the imputation statistics for each chromosome
Concatenate two input files into one
Gather the frequency statistics for each chromosome

Get all kandi verified functions for this library.

genipe Key Features

No Key Features are available at this moment for genipe.

genipe Examples and Code Snippets

No Code Snippets are available at this moment for genipe.

Community Discussions

Trending Discussions on genipe

Python program "genipe" - TypeError: __init__() got an unexpected keyword argument 'normalize'

QUESTION

Python program "genipe" - TypeError: __init__() got an unexpected keyword argument 'normalize'

Asked 2017-Jun-13 at 09:35

I am trying to run the program genipe to do some genome-wide survival analysis. I have installed genipe and all the relevant directories. However, when I go to run the program I get the error:

"TypeError: _ init _() got an unexpected keyword argument 'normalize'"

I haven't edited any of the genipe scripts and I have run genipe with no issues on a different server so I am not sure what is going wrong! Any help would be greatly appreciated.

Many thanks,

Caragh

Edit: I am using python version 3.6.1

Traceback as follows:

...

ANSWER

Answered 2017-Jun-01 at 10:31

Judging by the lifeline changelog this keyword argument has been removed from this particular function. Lifeline is a package which contains this particular function and is used by genipe.

You can either install previous version of lifeline by yourself and see if that will help or wait for updates in genipe library.

Looking at further errors from your comments, it seems like this is problematic code. You are trying to use dmatrices but it seems like it is not defined. Probably because mentioned try/catch block couldn't find statsmodel installed and therefore patsy wasn't imported either.

Try to install few more packages manually, starting with

and see if you will get any errors then...

Source https://stackoverflow.com/questions/44286247

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install genipe

You can install using 'pip install genipe' or download it from GitHub, PyPI.
You can use genipe like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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