Cyrius | A tool to genotype CYP2D6 with WGS data | Genomics library

by Illumina Python Version: v1.1.1 License: Apache-2.0

X-Ray Key Features Code Snippets(1)Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | Cyrius Summary

Cyrius is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. Cyrius has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Cyrius is a tool to genotype CYP2D6 from a whole-genome sequencing (WGS) BAM file. Cyrius uses a novel method to solve the problems caused by the high sequence similarity with the pseudogene paralog CYP2D7 and thus is able to detect all star alleles, particularly those that contain structural variants, accurately. Please refer to our paper for details about the method.

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Quality

Security

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Support

Cyrius has a low active ecosystem.

It has 22 star(s) with 2 fork(s). There are 10 watchers for this library.

It had no major release in the last 12 months.

There are 3 open issues and 5 have been closed. On average issues are closed in 17 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of Cyrius is v1.1.1

Quality

Cyrius has no bugs reported.

Security

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

License

Cyrius is licensed under the Apache-2.0 License. This license is Permissive.

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

Reuse

Cyrius releases are available to install and integrate.

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

Installation instructions are not available. Examples and code snippets are available.

Top functions reviewed by kandi - BETA

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

Perform D6 STAR calls
Calculate normalized normalization depth
Count reads for normalization
Calculate the normalized depth
Prepare resources for a given genome
Parse a hap file into a dictionary
Returns dictionary of SNPs
Make the variant set from variant list
Load command line parameters

Get all kandi verified functions for this library.

Cyrius Key Features

No Key Features are available at this moment for Cyrius.

Cyrius Examples and Code Snippets

Cyrius: WGS-based CYP2D6 genotyper,Running the program

Python

Lines of Code : 5

License : Permissive (Apache-2.0)

Copy

python3 star_caller.py --manifest MANIFEST_FILE \
                       --genome [19/37/38] \
                       --prefix OUTPUT_FILE_PREFIX \
                       --outDir OUTPUT_DIRECTORY \
                       --threads NUMBER_THREADS

Community Discussions

Trending Discussions on Cyrius

How with bash to get from a path all but the first folder

QUESTION

How with bash to get from a path all but the first folder

Asked 2018-Dec-16 at 14:12

How with bash to get from a path all but the first folder ?

e.g.

from 'a/b/d/e' to get 'b/d/e'

for now I do that with pythonpy

...

ANSWER

Answered 2018-Dec-16 at 11:52

With bash and its Parameter Expansion:

Source https://stackoverflow.com/questions/53801779

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

Vulnerabilities

No vulnerabilities reported

Install Cyrius

You can download it from GitHub.
You can use Cyrius 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

Common causes for Cyrius to produce no-calls are: -Low sequencing depth. We suggest a sequencing depth of 30x, which is the standard practice recommended by clinical genome sequencing. -The depth of the CYP2D6/CYP2D7 region is much lower than the rest of the genome, most likely because reads are aligned to alternative contigs. If your reference genome includes alternative contigs, we suggest alt-aware alignment so that alignments to the primary assembly take precedence over alternative contigs. -The majority of reads in CYP2D6/CYP2D7 region have a mapping quality of zero. This is probably due to some post-processing tools like bwa-postalt that modifies the mapQ in the BAM. We recommend using the BAM file before such post-processing steps as input to Cyrius.

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