ilus | handy variant calling pipeline generator | Genomics library

by ShujiaHuang Python Version: 2.0.0 License: GPL-3.0

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

kandi X-RAY | ilus Summary

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

A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.

Support

Quality

Security

License

Reuse

Support

ilus has a low active ecosystem.

It has 71 star(s) with 24 fork(s). There are 5 watchers for this library.

It had no major release in the last 12 months.

There are 2 open issues and 1 have been closed. On average issues are closed in 5 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ilus is 2.0.0

Quality

ilus has 0 bugs and 0 code smells.

Security

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

ilus code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

ilus 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

ilus releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

It has 1257 lines of code, 52 functions and 24 files.

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

Top functions reviewed by kandi - BETA

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

Recalibrate variantrecalibrator
Safely create a directory
Wrapper function for fname
Make a process shell
Wrapper for bwa_mem
Get bwa mem command
Convert fastq files into BAM
Create shell command
Generate markduplicates
Lazy load function
Extract sizes from a FASTA file
Genotypes from gVCF files
Find the overlap between two regions
Perform variant recalibrator recalibrate using gatk
Parse command line arguments
Check the status of all the jobs in the task log
Create gVCF files for gVCFs
Create WGS processes
Calibrate GATK basis
Extract non - n regions from a N region file
Helper function for gVC haplotype calls
Splits a shell file into sub - jobs

Get all kandi verified functions for this library.

ilus Key Features

No Key Features are available at this moment for ilus.

ilus Examples and Code Snippets

No Code Snippets are available at this moment for ilus.

Community Discussions

Trending Discussions on ilus

Java how to transform List to Page from JPA Paggination

Calculating group Standard Deviation in R, when you have groups with multiple data

QUESTION

Java how to transform List to Page from JPA Paggination

Asked 2021-Nov-29 at 01:00

I have a problem with my custom search method from Jpa Repository. I implement this method to custom serach and in this method i have List from my SQL base and i try to transform it to Page object from JPA Paggination & Sorting, but the way im trying to do this doesnt work. That is just an ilusion of pagination because in postman/internet browser i see all elements from list and when i change page and size value in endpoint that change nothing. Anybody know how to help?

GitHub project: https://github.com/s0bieskii/DemoCarRental

My endpoint from Controller:

...

ANSWER

Answered 2021-Nov-29 at 01:00

When you do custom queries and want to use Pageable, it's up to you to implement a logic to create a paging for your result list. In your case you aren't doing that so it's probably (you said it isn't working, but didn't say what isn't working so I can only guess) just returning the entire result list without paging applied.

A simple solution would be to use sublist and use the result of that operation as your parameter for PageImpl. Big problem is that you are still getting the entire result list from the database in the background which creates uneceassary overhead.

You could also adjust your query using

Source https://stackoverflow.com/questions/70147963

QUESTION

Calculating group Standard Deviation in R, when you have groups with multiple data

Asked 2021-May-17 at 16:22

I am working with R, and I am trying to calculate my standard deviation correctly.

My data look like this:

...

ANSWER

Answered 2021-May-17 at 16:22

Edit for sample data added:

While I'm not sure what you're trying to do, I can tell you are getting NAs there because you're asking for the SD of one number...which doesn't make sense. Ie...length(wordsproduced) will give you one number for the length, one category at a time.

I assume you want the SD of the number of wordsproduced per target, for each category.

So, you've calculated the mean wordsproduced per Target per category, as such:

Source https://stackoverflow.com/questions/67571475

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

Vulnerabilities

No vulnerabilities reported

Install ilus

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

Find more information at: