wgfast | Whole genome focused array SNP typer

by jasonsahl Python Version: Current License: No License

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kandi X-RAY | wgfast Summary

wgfast is a Python library typically used in Healthcare, Pharma, Life Sciences applications. wgfast has no bugs, it has no vulnerabilities, it has build file available and it has low support. You can download it from GitHub.

The whole genome focused array SNP typing (WG-FAST) pipeline written by: Jason Sahl Email: jasonsahl at gmail dot com. for a more comprehensive overview, look at the Manual. The goal of WG-FAST is to phylogenetically genotype an unknown sample in the context of a well studied pathogen. This sample can either be a metagenomics dataset, a metatranscriptomics dataset, or a single isolate sequencing dataset.

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Support

wgfast has a low active ecosystem.

It has 13 star(s) with 5 fork(s). There are 3 watchers for this library.

It had no major release in the last 6 months.

There are 3 open issues and 3 have been closed. On average issues are closed in 25 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of wgfast is current.

Quality

wgfast has 0 bugs and 0 code smells.

Security

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

wgfast code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

wgfast 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

wgfast 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.

wgfast saves you 1131 person hours of effort in developing the same functionality from scratch.

It has 2556 lines of code, 126 functions and 9 files.

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

Top functions reviewed by kandi - BETA

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

Perform workflow temprices
R Convert branch lengths to decimal places
Converts a matrix to a fasta file
Calculates the pairwise distances between taxonames
Run RAML - SSE - SSE3
Perform Bbduk work loop loop loop
Returns the length of a fastq file
Merges two files together
Make a matrix from a matrix
Subsample all SNPs from a matrix
Calculate the pairwise distances between taxonames
Prune the given tree
Insert a sequence into a fasta file
Extract the IDs from a fasta file
Calculate the base tree
Find used SNPs
Parse the distance file
Finds two new fields in the input file
Writes the reduced matrix to a reduced matrix
Transforms a phylogenetic tree
Runraxml on RAxSSE3
Compares two subsample results
Create parameters for a workflow create
Create parameter files
Reads in a set of fastq files into a dictionary
This method processes the temp matrix for the given distribution
Subsample SNPs from a matrix

Get all kandi verified functions for this library.

wgfast Key Features

No Key Features are available at this moment for wgfast.

wgfast Examples and Code Snippets

No Code Snippets are available at this moment for wgfast.

Community Discussions

No Community Discussions are available at this moment for wgfast.Refer to stack overflow page for discussions.

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

Vulnerabilities

No vulnerabilities reported

Install wgfast

You can download it from GitHub.
You can use wgfast 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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