seqpy | General utility functions for dealing with next generation

by murphycj Python Version: Current License: No License

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

kandi X-RAY | seqpy Summary

seqpy is a Python library. seqpy has no bugs, it has no vulnerabilities, it has build file available and it has low support. You can download it from GitHub.

General utility functions for dealing with next generation sequencing data

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Quality

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Support

seqpy has a low active ecosystem.

It has 0 star(s) with 0 fork(s). There are 1 watchers for this library.

It had no major release in the last 6 months.

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

It has a neutral sentiment in the developer community.

The latest version of seqpy is current.

Quality

seqpy has 0 bugs and 0 code smells.

Security

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

seqpy code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

seqpy does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

seqpy 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.

It has 3462 lines of code, 99 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 seqpy and discovered the below as its top functions. This is intended to give you an instant insight into seqpy implemented functionality, and help decide if they suit your requirements.

Initialize the ontology .
Creates a heatmap plot
Parse pathways .
Write unique pathways to a file .
Aggregate the data for each sample .
Plot top genes clustering .
Plot a bar chart .
Generates a pca plot for each group .
Create rk data from data
Count the number of reads in the junction sequence .

Get all kandi verified functions for this library.

seqpy Key Features

No Key Features are available at this moment for seqpy.

seqpy Examples and Code Snippets

No Code Snippets are available at this moment for seqpy.

Community Discussions

Trending Discussions on seqpy

What's the most efficient way to load k-mers into dict in python?

QUESTION

What's the most efficient way to load k-mers into dict in python?

Asked 2021-Apr-07 at 16:33

Currently, I have hundreds of bacterial genomes (fasta files), and I want to parse these fasta files then load k-mers from these files to a dict. For example,

A.fasta

...

ANSWER

Answered 2021-Apr-07 at 16:33

Demo code based on comments on original post. Process whole reverse complement at once instead of overlapping fragments iteratively.

Source https://stackoverflow.com/questions/66964755

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

Vulnerabilities

No vulnerabilities reported

Install seqpy

You can download it from GitHub.
You can use seqpy 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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