bohra | A pipeline for bioinformatics analysis of bacterial genomes | Genomics library

by kristyhoran Python Version: 2.3.6 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(4)Vulnerabilities Install Support

kandi X-RAY | bohra Summary

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

Bohra has a new look!. Bohra is microbial genomics pipeline, designed predominantly for use in public health, but may also be useful in research settings. The pipeline takes as input a tab-delimited file with the isolate IDs followed by the path to READ1 and READ2, a reference for alignment and a unique identifier, where reads are illumina reads (other platforms are not supported at this stage).

Support

Quality

Security

License

Reuse

Support

bohra has a low active ecosystem.

It has 23 star(s) with 7 fork(s). There are 4 watchers for this library.

There were 7 major release(s) in the last 12 months.

There are 11 open issues and 3 have been closed. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of bohra is 2.3.6

Quality

bohra has no bugs reported.

Security

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

License

bohra is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

bohra releases are not available. You will need to build from source code and install.

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.

Top functions reviewed by kandi - BETA

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

Compile report
Write table of distances
Writes data to pipeline
Get the genome from the image
Generate a summary table from tabdata
Merge two ds
Set the argument parser
Link a file to the working directory
Unzip the reference files
Generate the snpensity density plot
Adjust the offset of a row
Combine MLST files
Calculate a FASTA file
Combine Prokka files
Get the software version
Check Snippy s Snippy
Combine kraken files
Plot pairwise SNPs
Combine resistome
Parse seqtk output
Extract MLST locus from an isolate
Calculate core statistics from inputs
Helper function to fill values in a pipeline
Print the distances from a table
Combine assembly stats
Generate a dictionary for a given pipeline

Get all kandi verified functions for this library.

bohra Key Features

No Key Features are available at this moment for bohra.

bohra Examples and Code Snippets

No Code Snippets are available at this moment for bohra.

Community Discussions

Trending Discussions on bohra

Apply transition animation on navbar

Change color in sticky navbar using javascript

Multidimensional Array List Strange behavior

How to remove tag while printing in HTML?

QUESTION

Apply transition animation on navbar

Asked 2021-Mar-30 at 11:37

I have coded navbar to be sticky on scroll and change color as well. But all of the changes happen so suddenly and I have no idea how to improve that. Here are the code samples:

...

ANSWER

Answered 2021-Mar-30 at 11:20

Just add transition: background duration; property to navigation class. It will smooth out the background change.

Source https://stackoverflow.com/questions/66869895

QUESTION

Change color in sticky navbar using javascript

Asked 2021-Mar-30 at 07:22

I started with a white navbar background and as I scroll I change it to purple. Here, I want it to have white color of list items but I am unable to do that. Here's the full source codes in HTML, CSS and JS.

...

ANSWER

Answered 2021-Mar-30 at 06:53

You can simply target the element with this selector: .navigation.sticky > nav > ul > li > a and change the color to white. It will select the element of the navbar list when the .navigation div has the .sticky class as well.

Source https://stackoverflow.com/questions/66866017

QUESTION

Multidimensional Array List Strange behavior

Asked 2018-May-16 at 15:11

I really don't know what am I doing wrong here. I am gathering some data into an array of arrays of strings. In the end I get a duplicate answers instead of what I aspect.

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ANSWER

Answered 2018-May-16 at 15:11

I am very sorry for the duplicate, for some reason I didn't find the answer in two days of search so I open a new one.

Here : Why does my ArrayList contain N copies of the last item added to the list?

This pretty much explains why I got the error.

Source https://stackoverflow.com/questions/50352294

QUESTION

How to remove tag while printing in HTML?

Asked 2017-Nov-26 at 11:30

How to remove the link a tag when giving a print command?

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ANSWER

Answered 2017-Nov-26 at 11:25

you have to hide a[href]:after which is showing the link on print, so you could say:

Source https://stackoverflow.com/questions/47495475

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

Vulnerabilities

No vulnerabilities reported

Install bohra

Installing bohra with conda will ensure that all dependencies are present. See below for instructions on how to configure the databases for kraken2.
snakemake
Snippy
Shovill (skesa and spades.py)
Roary
Prokka
kraken2
abritamr
mlst
iqtree
seqtk
snp-dists
mash
The input file needs to be a tab-delimited file with three columns IsolateID, path to R1 and path to R2.
A closed reference from the same ST (where applicable) or a gold-standard reference (as may be used in M. tuberculosis).
A pacbio or nanopore assembly from MDU that is of the same type as the query dataset
A high quality de novo assembly of either an isolate in the dataset or an isolate of the same ST or type.

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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