drep | Rapid comparison and dereplication of genomes | Genomics library

by MrOlm Python Version: 3.5.0 License: No License

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

kandi X-RAY | drep Summary

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

dRep is a python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set. Manual, installation instructions, and API are at available at ReadTheDocs. Publication is available at ISMEJ. Open source pre-print publication is available at bioRxiv.

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drep has a low active ecosystem.

It has 160 star(s) with 32 fork(s). There are 7 watchers for this library.

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

There are 9 open issues and 157 have been closed. On average issues are closed in 39 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of drep is 3.5.0

Quality

drep has 0 bugs and 0 code smells.

Security

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

drep code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

drep 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

drep 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 are not available. Examples and code snippets are available.

drep saves you 3790 person hours of effort in developing the same functionality from scratch.

It has 5903 lines of code, 351 functions and 37 files.

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

Top functions reviewed by kandi - BETA

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

Define dereplicate step
Wrapper around dendrogram
Generate the Mash Dendrogram from a wdb file
Parse options
Parse command line arguments
Prints help
Runs pairwise gANI calculation
Return the path to the directory
Performs greedy clustering
Generate a greedy cluster
Parse the results
Prints the time estimate of the time of the two databases
Parse a nsimscan file and return a pandas dataframe
Run the cluster
Run secondary clustering
Greedy clustering
Generate a genome from a list of sequences
Duplicate scaffolds
Run pairwise fastan fastani
Wrapper for cluster test tests
Perform clustering on ANIn database
Run the MASH command on all genomes
Perform pairwise ANImImf
Run pairwise ANIn
Run goANI command - line tool
Extract scaffold

Get all kandi verified functions for this library.

drep Key Features

No Key Features are available at this moment for drep.

drep Examples and Code Snippets

No Code Snippets are available at this moment for drep.

Community Discussions

Trending Discussions on drep

Dynamic queries and JpaSpecificationExecutor in Spring

Agda not eliminating clause in goal despite pattern matching on it

how to print derivatives more compactly (subscript notation)

QUESTION

Dynamic queries and JpaSpecificationExecutor in Spring

Asked 2021-Dec-31 at 23:12

I am trying to create a simple Spring project where restaurants can add menu items to shared database and users can use a html form to search the dishes based on a range of criteria- especially dietary requirements

Form example:

...

ANSWER

Answered 2021-Dec-20 at 19:15

I believe the issue is that you are not adding the result in the Model which is being used to render the page show_dish_List.html, therefore nothing is being populated in the UI. Your UI is expecting the data to be in listDishSearch and there is nothing in that variable.

Update your code to:

Source https://stackoverflow.com/questions/70415803

QUESTION

Agda not eliminating clause in goal despite pattern matching on it

Asked 2021-May-06 at 11:20

I have a snippet of agda code of the following form:

...

ANSWER

Answered 2021-May-06 at 11:20

I believe the below snippet models your problem accurately:

Source https://stackoverflow.com/questions/67282594

QUESTION

how to print derivatives more compactly (subscript notation)

Asked 2020-Apr-28 at 11:39

currently I'm struggeling a little bit with the output from SymPy. By default, by executing the following (assuming using Jupyter Notebook):

...

ANSWER

Answered 2020-Apr-23 at 11:22

The Derivative (like all SymPy objects) has arguments -- sometimes named -- and you can do with those whatever is useful to you. In this case it looks like replacing the function with a letter and the derivative variables as a composite symbol is what you want. Here is an attempt at that that can be tweaked as necessary:

Source https://stackoverflow.com/questions/61385668

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

Vulnerabilities

No vulnerabilities reported

Install drep

You can install using 'pip install drep' or download it from GitHub, PyPI.
You can use drep 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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