platon | bacterial plasmid-borne contigs | Genomics library

by oschwengers Python Version: v1.6 License: GPL-3.0

X-Ray Key Features Code Snippets(3)Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | platon Summary

platon is a Python library typically used in Artificial Intelligence, Genomics applications. platon 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 platon' or download it from GitHub, PyPI.

TL;DR Platon detects plasmid contigs within bacterial draft genomes from WGS short-read assemblies. Therefore, Platon analyzes the natural distribution biases of certain protein coding genes between chromosomes and plasmids. This analysis is complemented by comprehensive contig characterizations upon which several heuristics are applied.

Support

Quality

Security

License

Reuse

Support

platon has a low active ecosystem.

It has 80 star(s) with 14 fork(s). There are 4 watchers for this library.

It had no major release in the last 12 months.

There are 2 open issues and 32 have been closed. On average issues are closed in 33 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of platon is v1.6

Quality

platon has 0 bugs and 0 code smells.

Security

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

platon code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

platon 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

platon 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.

Top functions reviewed by kandi - BETA

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

Validate dependencies
Read the tool output from a tool
Validate the version
Sets up NCBI
Calculate RDS p - value

Get all kandi verified functions for this library.

platon Key Features

No Key Features are available at this moment for platon.

platon Examples and Code Snippets

Platon: identification and characterization of bacterial plasmid contigs from short-read draft assemblies.,Usage

Python

Lines of Code : 28

License : Strong Copyleft (GPL-3.0)

Copy

usage: platon [-h] [--db DB] [--mode {sensitivity,accuracy,specificity}]
              [--characterize] [--output OUTPUT] [--prefix PREFIX]
              [--threads THREADS] [--verbose] [--version]
              

Identification and characterization

Platon: identification and characterization of bacterial plasmid contigs from short-read draft assemblies.,Installation,Database download

Python

Lines of Code : 8

License : Strong Copyleft (GPL-3.0)

Copy

$ wget https://zenodo.org/record/4066768/files/db.tar.gz
$ tar -xzf db.tar.gz
$ rm db.tar.gz

$ platon --db  genome.fasta

$ export PLATON_DB=
$ platon genome.fasta

$ cp -r db/

Platon: identification and characterization of bacterial plasmid contigs from short-read draft assemblies.,Examples

Python

Lines of Code : 2

License : Strong Copyleft (GPL-3.0)

Copy

$ platon genome.fasta

$ platon -db ~/db --output results/ --verbose --threads 8 genome.fasta

Community Discussions

Trending Discussions on platon

Create std::chrono::zoned_time from zone and time

ReactJS : How to useParams?

Why is the ratio of the Surface Area to Volume Ratios of a Octahedron and Cube, a constant, not reflected in my program?

Extract specific keywords from XML file with bash script

CSS resize property: Resize all elements simultaneously?

QUESTION

Create std::chrono::zoned_time from zone and time

Asked 2022-Jan-18 at 22:19

I have a datetime in a platonic sense, i.e some date and time (like 18th of January 2022 15:15:00) and I know in which timezone it represent something, e.g "Europe/Moscow"

I want to create std::chrono::zoned_time. Is is possible? I looked at the constructors and it seems all of them require either sys_time or local_time which is not what I have.

Am I missing something obvious?

...

ANSWER

Answered 2022-Jan-18 at 17:25

#include 
#include 

int
main()
{
    using namespace std::literals;
    std::chrono::zoned_time zt{"Europe/Moscow",
        std::chrono::local_days{18d/std::chrono::January/2022} + 15h + 15min};
    std::cout << zt << '\n';
}

Source https://stackoverflow.com/questions/70755499

QUESTION

ReactJS : How to useParams?

Asked 2021-Aug-10 at 23:08

Im kinda struggling with a simple filter method on ReactJS.

Whenever I use the useParams it brokes my filter function.

I find no documentation/tutorials without incrementations or buttons about useEffect & useState.

I hope anyone can help, thanks.

Details.js

...

ANSWER

Answered 2021-Aug-10 at 22:03

Note that useParams returns key-value pairs. Maybe destructuring it will help? Like this:

let { name } = useParams() instead of let name = useParams()

Source https://stackoverflow.com/questions/68733901

QUESTION

Why is the ratio of the Surface Area to Volume Ratios of a Octahedron and Cube, a constant, not reflected in my program?

Asked 2021-Apr-22 at 03:12

I've reached a wall in publishing my paper due to the issue of two platonic solids I'm coding for their SA:V: The cube and octahedron.

Normally, when one derivates the SA:V ratio for a cube and octahedron, it will come out to 6/a and (3*sqrt(6))/a, respectively.

When you take those ratios as a ratio, you get a constant non 1:1 ratio for all size regimes so, how is my output a 1:1 relationship?

Output (click link):

Graph of Ratios:

Table

Relevant code for both shapes in all instances for user request, tabulation, and graphing (ignore icosahedron code): First Instance:

...

ANSWER

Answered 2021-Apr-22 at 03:12

You are calculating "Surface Area to Volume Ratio of Platonic Polyhedra Against Referential Sphere for Given Diameter" [boldface added]

So before you compare the cube to the octahedron, you compare the cube to the sphere of the cube's diameter, and the octahedron to the sphere of the octahedron's diameter.

(I presume this means circumscribed spheres; I'm not going to check inscribed spheres.)

The SA/V ratio of a sphere is 6/d, where d is the diameter.

The maximum diameter of a cube of edge-length a is sqrt(3)a, so the cube/sphere ratio is (6/a)/(6/(sqrt(3)a)) = sqrt(3)

The maximum diameter of an octahedron of edge-length a is sqrt(2)a, so the octahedron/sphere ratio is (3sqrt(6)/a)/(6/(sqrt(2)a)) = sqrt(3)

So the ratio comes out to 1:1, due to the comparison to spheres.

Source https://stackoverflow.com/questions/67205288

QUESTION

Extract specific keywords from XML file with bash script

Asked 2020-Dec-05 at 15:50

I have an XML file containing some entries characterized by specific kaywords. I need to run a for loop on the entries, extract two different keywords for each for them to be used in the for loop as variables.

Here is an example of list.xml:

...

ANSWER

Answered 2020-Nov-27 at 14:24

Command:

Source https://stackoverflow.com/questions/65037044

QUESTION

CSS resize property: Resize all elements simultaneously?

Asked 2020-Nov-26 at 12:27

Given a page which has say 5 textboxes, resizable in height with the css resize property.

If the user resizes one of them, all 5 textboxes should resize simultaneously.

How to achive that?

...

ANSWER

Answered 2020-Nov-25 at 20:51

Can't find a way to do this in pure CSS so put here a JS/CSS solution in case it is of help.

Basically we use the ResizeObserver method to catch a resize on a textarea and update the heights of the other textareas. We don't let more than one area's resize be coped with at a time else there can be some unwanted looping.

Source https://stackoverflow.com/questions/65005964

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

Vulnerabilities

No vulnerabilities reported

Install platon

Platon can be installed via BioConda or Pip. However, we encourage to use Conda to automatically install all required 3rd party dependencies. In all cases a mandatory database must be downloaded.
Platon requires a mandatory database which is publicly hosted at Zenodo: Further information is provided in the database section below.

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 .

Find more information at: