bipy | DEPRECATED Lightweight bioinformatics pipeline tools | Genomics library

by roryk Python Version: Current License: MIT

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

kandi X-RAY | bipy Summary

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

This is an alpha set of wrappers around commonly-used bioinformatics tools to run bioinformatics pipelines using IPython to handle parallelization across cores and nodes. Uses several wrappers and ideas from and will eventually be merged into it. This documentation is not complete yet.

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Quality

Security

License

Reuse

Support

bipy has a low active ecosystem.

It has 14 star(s) with 8 fork(s). There are 4 watchers for this library.

It had no major release in the last 6 months.

bipy has no issues reported. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of bipy is current.

Quality

bipy has 0 bugs and 0 code smells.

Security

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

bipy code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

bipy is licensed under the MIT License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

bipy 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.

Installation instructions, examples and code snippets are available.

bipy saves you 2088 person hours of effort in developing the same functionality from scratch.

It has 4581 lines of code, 456 functions and 59 files.

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

Top functions reviewed by kandi - BETA

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

Start the cluster
Get the client
Return direct access to the client
Return True if the controller is up
Add attribute to a GTF file
Convert an attribute to a dictionary
Filters out lines that are shorter than the maximum length
Calculate transcript lengths
Convert a panda table to a LaTeX table
Make a latex table header
Convert samtools to BAM
Sort a list of GTF lines by transcript
Delete attributes from a list of attributes
Perform multi intersecting
Intersect two input files
Parse a GTF file into a dictionary
Get the top gene table
Replaces the attributes in the source line with replace
Filters the attributes in a file
Setup pipeline configuration
Filters the given list of lines with shorter than size
Iterate over all registered plugins
Process all files in the queue
Remove all reads that are shorter than min_length
Setup logging
Convert a BAM file into a SAM file

Get all kandi verified functions for this library.

bipy Key Features

No Key Features are available at this moment for bipy.

bipy Examples and Code Snippets

No Code Snippets are available at this moment for bipy.

Community Discussions

Trending Discussions on bipy

Python: Relative imports

QUESTION

Python: Relative imports

Asked 2021-May-14 at 10:08

I'm trying to use a package that has the following structure:

The file prova.py contains only the following line:

...

ANSWER

Answered 2021-May-14 at 10:08

It looks like you're using this: https://github.com/tpoisot/bipy and that prova.py is your addition (it would be nice if you include this kind of information in your question in future questions!)

The problem is that bipartite_class is not a free-standing module, but is a part of the package bipy. That means you need to import it from outside the package. You need to move prova.py one directory up, to bipy-master, and change its contents to:

Source https://stackoverflow.com/questions/67532203

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

Vulnerabilities

No vulnerabilities reported

Install bipy

It will take a small bit of fiddling around to get everything working as there are a couple of pieces that need to interact together properly to work. You can get going testing everything locally by setting up a default IPython profile to run on your local machine.

Support

If the cluster unit test is failing, something might not be set up properly with IPython. First, test to see that IPython is functioning correctly: ipcluster start --n=4 --profile=bipy_test.

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