thinspace | free method to dereplicate massive genome collections | Genomics library

by phiweger Python Version: Current License: BSD-3-Clause

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | thinspace Summary

thinspace is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. thinspace has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However thinspace build file is not available. You can download it from GitHub.

Many recent microbial genome collections curate hundreds of thousands of genomes. This volume complicates many genomic analyses such as taxon assignment because the associated computational burden is substantial. However, the number of representatives of each species is highly skewed towards human pathogens and model organisms. Thus many genomes contain little additional information and could be removed. We created a frugal dereplication method that can reduce massive genome collections based on genome sequence alone, without the need for manual curation nor taxonomic information.

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Support

thinspace has a low active ecosystem.

It has 8 star(s) with 0 fork(s). There are 1 watchers for this library.

It had no major release in the last 6 months.

There are 1 open issues and 0 have been closed. On average issues are closed in 282 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of thinspace is current.

Quality

thinspace has no bugs reported.

Security

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

License

thinspace is licensed under the BSD-3-Clause License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

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

thinspace has no build file. You will be need to create the build yourself to build the component from source.

Installation instructions, examples and code snippets are available.

Top functions reviewed by kandi - BETA

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

Load taxonomic taxonomies
Get all ancestors of tax_id
Return the open function for the given filename
Determine the compression type of a file
Process single taxon assembly
De - replicate assembly
Finds the assembly file for each accession
Write taxonomy nodes to file
Returns the label for a taxon taxon
Get rank from taxon name
Given a list of accessions find all assembly files
Find the assembly filename based on accession
Assign taxa to taxa
Create taxonomy names file
Return a set of taxon names used in taxon
Load a tree
Check if arguments are valid
Create concatenated FASTA file
Calculate the count of tax_ids for each tax
Count reads in a fastq file
Write a summary summary file
Write a conversion table
Make a directory of the assembly files
Load GTDB taxonomy
Writes a classification counts table
Parse arguments
Load tax ids per read
Duplicate assembly

Get all kandi verified functions for this library.

thinspace Key Features

No Key Features are available at this moment for thinspace.

thinspace Examples and Code Snippets

No Code Snippets are available at this moment for thinspace.

Community Discussions

Trending Discussions on thinspace

"String.replace" does not work for unicode notations

How to save unicode character in SQL database

QUESTION

"String.replace" does not work for unicode notations

Asked 2020-Jul-27 at 00:27

I expect that the function buildAllKindsOfSpaceCharactersSetExpression will replace \\u{2002}\\u{2003}\\u{2004}\\u{2005}\\u{2006}\\u{2007}\\u{2008}\\u{2009} to \\u{2002}-\\u{2009}. Why it does not happen?

...

ANSWER

Answered 2020-Jul-27 at 00:27

Found the mistake:

Source https://stackoverflow.com/questions/63106995

QUESTION

How to save unicode character in SQL database

Asked 2019-Jan-13 at 15:47

I am trying to save ThinSpace (\u2009) to the database using ADO.NET classes, but instead I am getting "?" symbol in db in place of ThinSpace. String that I save to db in UTF8 format.

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ANSWER

Answered 2019-Jan-13 at 15:09

may be this might help:

Source https://stackoverflow.com/questions/54169985

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

Vulnerabilities

No vulnerabilities reported

Install thinspace

There are a couple of dependencies, we apologize -- on the other hand, thinspace will embed genomes, cluster them, assess cluster quality, dereplicate them using k-mer hashes and finally create a Centrifuge index for direct use.

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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