GroopM | Metagenomic binning suite | Genomics library

by Ecogenomics Python Version: Current License: GPL-3.0

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

kandi X-RAY | GroopM Summary

GroopM is a Python library typically used in Artificial Intelligence, Genomics applications. GroopM has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

GroopM is a metagenomic binning toolset. It leverages spatio-temoral dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets. GroopM is largely parameter-free. Use: groopm -h for more info. For installation and usage instructions see : Data preparation and running GroopM. Project home page, info on the source tree, documentation, issues and how to contribute, see If you use this software then we’d love you to cite us. Our paper is now available at The DOI is Copyright 2012-2015 Michael Imelfort. GroopM is licensed under the GNU GPL v3 See LICENSE.txt for further details.

Support

Quality

Security

License

Reuse

Support

GroopM has a low active ecosystem.

It has 24 star(s) with 16 fork(s). There are 12 watchers for this library.

It had no major release in the last 6 months.

There are 21 open issues and 12 have been closed. On average issues are closed in 85 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of GroopM is current.

Quality

GroopM has 0 bugs and 0 code smells.

Security

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

GroopM code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

GroopM is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

GroopM releases are not available. You will need to build from source code and install.

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

Top functions reviewed by kandi - BETA

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

Perform two way - way two - way intersection .
Create a new database .
Parse options .
Find merge groups .
Render the TransCPData .
Perform the hough partition of the data .
Train the SOM .
Plots the contigs for each bin
Shuffle the bams in place .
Plot data for multiple bins .

Get all kandi verified functions for this library.

GroopM Key Features

No Key Features are available at this moment for GroopM.

GroopM Examples and Code Snippets

No Code Snippets are available at this moment for GroopM.

Community Discussions

Trending Discussions on GroopM

Try/except still throws error in try block

QUESTION

Try/except still throws error in try block

Asked 2018-Dec-07 at 01:14

while running groopm program from https://github.com/Ecogenomics/GroopM, I encountered the following error :

...

ANSWER

Answered 2018-Dec-07 at 01:14

Your except block does not handle the error being raised. It is set to handle a np.linalg.linalg.LinAlgError, but the error being raised is a FloatingPointError.

Change your code to catch either exception:

Source https://stackoverflow.com/questions/53661428

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

Vulnerabilities

No vulnerabilities reported

Install GroopM

You can download it from GitHub.
You can use GroopM 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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