pybedtools | Python wrapper -- and more -- for Aaron Quinlan | Genomics library

by daler Python Version: 0.9.1 License: Non-SPDX

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

kandi X-RAY | pybedtools Summary

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

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

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pybedtools has a low active ecosystem.

It has 243 star(s) with 89 fork(s). There are 18 watchers for this library.

It had no major release in the last 12 months.

There are 12 open issues and 241 have been closed. On average issues are closed in 156 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of pybedtools is 0.9.1

Quality

pybedtools has 0 bugs and 0 code smells.

Security

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

pybedtools code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

pybedtools 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

pybedtools releases are available to install and integrate.

Deployable package is available in PyPI.

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

Top functions reviewed by kandi - BETA

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

Wrapper for BEDTools
Handle keyword arguments
Check if genome is set
Create temporary file
Tags a BEDPE
Return the number of fields in the dataset
Intersection intersect
Generate a pie plot
Removes invalid features
Apply method to BEDTool
Wrapper for parallelization
Plot two BedTool objects
Add a new xstream
Try to download setuptools
Compute the absolute distance between two points
Calculate the probability intersection between two genomes
Return a list of vertices
Return the distance between two features
Creates a Venn plot based on BedTool
Convert a bam to a bigwig
Generate a Venn diagram
Calculate random jaccard distribution
Generate a venn plot of two regions
Remove invalid features from the bed file
Create a BedTool object from a pandas dataframe
Generate a matrix for each file
Run a bigbed file on a genome

Get all kandi verified functions for this library.

pybedtools Key Features

No Key Features are available at this moment for pybedtools.

pybedtools Examples and Code Snippets

No Code Snippets are available at this moment for pybedtools.

Community Discussions

Trending Discussions on pybedtools

Mocking class methods, still running the original method with some wrapped code

QUESTION

Mocking class methods, still running the original method with some wrapped code

Asked 2021-Jun-20 at 08:14

I want to patch a method by running the original method with additional code before and after. In particular, I'm running tests within a pyfakefs in-memory file system, but I want to sometime use the real file system because some packages will not work on the fake file system (pybedtools in my case).

There is probably simple way to do this, but I can't figure it out after many, many tries. Is this possible?

Just for an example, below I'm trying to patch to_csv in pandas.

...

ANSWER

Answered 2021-Jun-20 at 08:14

One (not very elegant) possibility would be to use the third approach and avoid the recursion by using the old saved to_csv method:

Source https://stackoverflow.com/questions/68049868

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

Vulnerabilities

No vulnerabilities reported

Install pybedtools

You can install using 'pip install pybedtools' or download it from GitHub, PyPI.
You can use pybedtools 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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