kaeaton/gsg-kotlin

A search tool for GFE names of HLA and KIR genes.

GFE Search Generator

There are currently tens of thousands of known variants of the Human Leukocyte Antigen (HLA) genes, the genes most responsible for transplant success or failure, with new variants (known as “alleles”) being discovered and “named” every day. The current names give very little information about the structure of the proteins encoded by these genes, and in 2015, Dr. Steven Mack proposed a new naming convention called Gene Feature Enumeration (GFE). New tools are required to use the new GFE naming convention, including (1) the ability to switch between the HLA allele names and the GFE names, (2) search through the GFE names, and (3) assign GFE names to new alleles.

The project is built using Kotlin, JVM 17, OpenJavaFX 0.0.9, and TornadoFX, bundled together with Gradle.

gsg-kotlin's Issues

Leave search query in GFE search upon submitting data, add reset button

Use soft reset for "Reset All button".

Add file type selector and write to file checkbox

Start with CSV and TSV. Pretty can be added later.

Downloading raw data

Set GFE as keys.
Scan for duplicates before writing a new key/value pair.

BuildRegexString in GFESearch - refactor to use StringBuilder

KIR processing

Needs to skip missing exons/introns when building the headers and regex.

Decisions need to be made about how to present this data in the header string, and in the results, both on the screen and in the results file.

When changing versions, if there is no data for the previously selected locus, select 1st item in locus list.