CNVpytor | python extension of CNVnator | Genomics library

by abyzovlab Python Version: 1.3.1 License: MIT

X-Ray Key Features Code Snippets(3)Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | CNVpytor Summary

CNVpytor is a Python library typically used in Artificial Intelligence, Genomics applications. CNVpytor has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. However CNVpytor has 4 bugs. You can install using 'pip install CNVpytor' or download it from GitHub, PyPI.

CNVpytor is a Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads developed in Abyzov Lab, Mayo Clinic. Follow CNVpytor Twitter account.

Support

Quality

Security

License

Reuse

Support

CNVpytor has a low active ecosystem.

It has 77 star(s) with 8 fork(s). There are 7 watchers for this library.

There were 1 major release(s) in the last 12 months.

There are 20 open issues and 86 have been closed. On average issues are closed in 29 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of CNVpytor is 1.3.1

Quality

CNVpytor has 4 bugs (0 blocker, 0 critical, 0 major, 4 minor) and 212 code smells.

Security

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

CNVpytor code analysis shows 0 unresolved vulnerabilities.

There are 16 security hotspots that need review.

License

CNVpytor 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

CNVpytor releases are available to install and integrate.

Deployable package is available in PyPI.

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

Installation instructions, examples and code snippets are available.

It has 24902 lines of code, 203 functions and 29 files.

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

Top functions reviewed by kandi - BETA

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

Calls 2d - phase 2d
Generate an extended chromosome name
Return a canonical chromosome name
Return True if the given chromosome is a autosome
Call 2d SNPs
Compute the p - value p - value p - value
Compute the likelihood overlap between two sequences
Compute the likelihood of a baf
Prompt the user for input files
Compare two histograms
Calculate rd_stat
Calculate BAF histogram for each chromosome
Perform a genome call
Calculate histograms for each bin
Calculate histograms based on bin sizes
Calls BAF phase
Call BAFs
Compare two regions
Compare two BAF files
Generate a callmap for each chromosome
Compare two SNPs
Partition a sequence of bin sizes
Calculate BAF likelihoods for each bin
Generate a callmap for each region
Wrapper for single cell allele dropout
Phase SNPs
Performs mosaic analysis

Get all kandi verified functions for this library.

CNVpytor Key Features

No Key Features are available at this moment for CNVpytor.

CNVpytor Examples and Code Snippets

CNVpytor - a python extension of CNVnator,Use as a command line tool,Plot from interactive mode

Python

Lines of Code : 64

License : Permissive (MIT)

Copy

> cnvpytor -root file.pytor -view 10000
cnvpytor> chr1:1M-50M
cnvpytor> rd
cnvpytor> set panels rd likelihood
cnvpytor> show
Parameters
    * baf_colors: ['gray', 'black', 'red', 'green', 'blue']
    * bin_size: 100000
    * chrom: []

CNVpytor - a python extension of CNVnator,Use as a command line tool,Merging calls form multiple samples

Python

Lines of Code : 19

License : Permissive (MIT)

Copy

> cnvpytor -root file1.pytor file2.pytor ... -view 100000 
print joint_calls
set Q0_range 0 0.5
set size_range 100000 inf
set print_filename output.xls
print joint_calls

> cnvpytor -root file1.pytor file2.pytor ... -view 100000 
set Q0_range 0

CNVpytor - a python extension of CNVnator,Use as a command line tool,Filtering calls form view mode

Python

Lines of Code : 16

License : Permissive (MIT)

Copy

> cnvpytor -root file.pytor -view 100000 
print calls
set Q0_range 0 0.5
set size_range 100000 inf
print calls
set p_range 0 0.00001
set print_filename output.xls
print calls
set print_filename output.vcf
print calls

> cnvpytor -root file.pyto

Community Discussions

Trending Discussions on CNVpytor

How to execute the command in another bash prompt in Perl?

QUESTION

How to execute the command in another bash prompt in Perl?

Asked 2022-Feb-28 at 18:49

I am working on CnvPytor and trying to automate some commands using Perl. But it is not working because when I give first command it is going inside another bash prompt (cnvpytor). Please refer the below screenshot,

I have written the below script, but it is not working

...

ANSWER

Answered 2022-Feb-21 at 14:45

Each backtick pair runs a separate process.

I have no idea what CnvPytor is (and the link you provided doesn't help much), but the usual way is to run the external tool using some kind of IPC to communicate with it.

Source https://stackoverflow.com/questions/71208147

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

Vulnerabilities

No vulnerabilities reported

Install CNVpytor

For single user (without admin privileges) use:.
Old version (v1.0) is available using pip directly (not recomended):.

Support

Please report any bugs that you find on GitHub: https://github.com/abyzovlab/CNVpytor/issues. Or, even better, fork the repository on GitHub and create a pull request.

Find more information at: