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TheJacksonLaboratory / vmvt

vmvt: variant-motif visualization tool
https://vmvt.readthedocs.io/en/latest/index.html
BSD 3-Clause "New" or "Revised" License
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vmvt

Variant Motif Visualization Tool: Create SVG plots to represent splice variants

Requirements

Vmvt is a Java 11 library with no external dependencies.

First, add vmvt into your project, i.e. add the following into the pom.xml of your Maven project:

<dependency>
    <groupId>org.monarchinitiative.vmvt</groupId>
    <artifactId>vmvt-core</artifactId>
    <version>0.9.4</version>
</dependency>

Vmvt can be used in both modular and non-modular Java applications.

Usage

// Sequence of a reference and alternate donor site
final String ref = "AAGGTCAGA";
final String alt = "AAGATCAGA";
VmvtGenerator vmvt = new VmvtGenerator();
String dist = vmvt.getDonorDistributionSvg(ref, alt);
String donor = vmvt.getDonorLogoSvg(ref,alt);

The output

Vmvt produces SVG visualizations of the predicted effects of splice variants. Here is an example variant at the +1 position of a donor sequence.

donor vmvt image

Kick the tires

In the class org.monarchinitiative.vmvt.svg.DonorWriterTest, two SVGs can be created

testWriteDonorSvgLogo() 
testWriteDonorSvgWalker()

Running the test will create two local files in this directory, walkertest.svg and logotest.svg that can be viewed in a browser for convenience. There is an analogous test for acceptors.