PharmCAT | The Pharmacogenomic Clinical Annotation Tool | Data Labeling library

by PharmGKB Java Version: 0.3.0 License: MPL-2.0

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

kandi X-RAY | PharmCAT Summary

PharmCAT is a Java library typically used in Artificial Intelligence, Data Labeling applications. PharmCAT has no bugs, it has no vulnerabilities, it has build file available, it has a Weak Copyleft License and it has low support. You can download it from GitHub, Maven.

A tool to extract all CPIC guideline gene variants from a genetic dataset (represented as a VCF file), interpret the variant alleles, and generate a report.

Support

Quality

Security

License

Reuse

Support

PharmCAT has a low active ecosystem.

It has 88 star(s) with 32 fork(s). There are 27 watchers for this library.

It had no major release in the last 12 months.

There are 21 open issues and 104 have been closed. On average issues are closed in 117 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of PharmCAT is 0.3.0

Quality

PharmCAT has 0 bugs and 0 code smells.

Security

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

PharmCAT code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

PharmCAT is licensed under the MPL-2.0 License. This license is Weak Copyleft.

Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

Reuse

PharmCAT releases are available to install and integrate.

Deployable package is available in Maven.

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

PharmCAT saves you 7224 person hours of effort in developing the same functionality from scratch.

It has 14940 lines of code, 837 functions and 111 files.

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

Top functions reviewed by kandi - BETA

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

Command line parser
Deserialize a set of VCF exclusions from a TV file
Generate the allele definitions
Translate a variant locator to VCF data
Parses a line in VCF
Validate allele
Normalizes the alleles in VCF
Find all annotations that are compatible with the annotation
Finds annotations for the evidence
Main entry point
Implements the comparator
Add a phenotype to the diplotype
Initialize the matcher
Compare two configurations
Runs the program
Convert genotype to rx phenotype
Checks if a message matches a given gene annotation
Normalize a phenotype value
Infer the list of diplotypes that should be used
Compare two characters
Calculates the locations of all locations of a gene
Builds the messages from a gene call
Read VCF file
Compares two strings
Compares two based names
The main entry point

Get all kandi verified functions for this library.

PharmCAT Key Features

No Key Features are available at this moment for PharmCAT.

PharmCAT Examples and Code Snippets

No Code Snippets are available at this moment for PharmCAT.

Community Discussions

Trending Discussions on Data Labeling

How can I do this split process in Python?

Replacing a character with a space and dividing the string into two words in R

Azure ML FileDataset registers, but cannot be accessed for Data Labeling project

QUESTION

How can I do this split process in Python?

Asked 2021-Dec-30 at 14:06

I'm trying to make a data labeling in a table, and I need to do it in such a way that, in each row, the index is repeated, however, that in each column there is another Enum class.

What I've done so far is make this representation with the same enumerator class.

A solution using the column separately as a list would also be possible. But what would be the best way to resolve this?

...

ANSWER

Answered 2021-Dec-30 at 13:57

Instead of using Enum you can use a dict mapping. You can avoid loops if you flatten your dataframe:

Source https://stackoverflow.com/questions/70532286

QUESTION

Replacing a character with a space and dividing the string into two words in R

Asked 2020-Nov-18 at 07:32

I have a dataframe that contains a column that includes strings separeted with semi-colons and it is followed by a space. But unfortunately in some of the strings there is a semi-colon that is not followed by a space.

In this case, This is what i'd like to do: If there is a space after the semi-colon we do not need a change. However if there are letters before and after the semi-colon, we should change semi-colon with space

i have this:

...

ANSWER

Answered 2020-Nov-16 at 07:24

Try something like:

Source https://stackoverflow.com/questions/64853962

QUESTION

Azure ML FileDataset registers, but cannot be accessed for Data Labeling project

Asked 2020-Oct-28 at 20:31

Objective: Generate a down-sampled FileDataset using random sampling from a larger FileDataset to be used in a Data Labeling project.

Details: I have a large FileDataset containing millions of images. Each filename contains details about the 'section' it was taken from. A section may contain thousands of images. I want to randomly select a specific number of sections and all the images associated with those sections. Then register the sample as a new dataset.

Please note that the code below is not a direct copy and paste as there are elements such as filepaths and variables that have been renamed for confidentiality reasons.

...

ANSWER

Answered 2020-Oct-27 at 22:39

Is the data behind virtual network by any chance?

Source https://stackoverflow.com/questions/64546521

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

Vulnerabilities

No vulnerabilities reported

Install PharmCAT

You can download it from GitHub, Maven.
You can use PharmCAT like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the PharmCAT component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer maven.apache.org. For Gradle installation, please refer gradle.org .