https://github.com/sammyjava/pangenomics

Java code writtten for pangenomics work
https://github.com/sammyjava/pangenomics

Last synced: 1 day ago
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Java code writtten for pangenomics work

• Host: GitHub
• URL: https://github.com/sammyjava/pangenomics
• Owner: sammyjava
• License: mit
• Created: 2020-05-29T13:30:03.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2022-01-05T13:53:14.000Z (about 3 years ago)
• Last Synced: 2024-11-11T09:50:13.467Z (2 months ago)
• Language: Java
• Size: 5.52 MB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
This directory contains classes for working with pan-genomic graphs and frequented regions, based on the paper

```

Cleary, et al., "Exploring Frequented Regions in Pan-Genomic Graphs", IEEE/ACM Trans Comput Biol Bioinform. 2018 Aug 9. PMID:30106690 DOI:10.1109/TCBB.2018.2864564

``` 

This work was funded in part by the National Center for Genome Resources, Santa Fe, NM.

## Building

The project is set up with dependencies managed with the [Gradle build tool](https://gradle.org/). To build the distribution, simply run

```

$ ./gradlew installDist

```

This will create a distribution under `build/install` that is used by the various run scripts.

### org.ncgr.pangenomics

This contains two packages with similarly-named classes:

**org.ncgr.pangenomics.allele** which contains classes for working with allele-based sequence graphs

**org.ncgr.pangenomics.genotype** which contains classes for working with genotype graphs

Basic graph-related classes, not particularly specific to frequented regions:

`PangenomicGraph` extends org.jgrapht.graph.DirectedAcyclicGraph and stores a graph with methods for reading it in from files and various output methods.

There is a `main` class for creating a graph from input data such as a GFA or VCF file.

`Node` encapsulates a node in a Graph: its ID (a long) and, for sequence graphs, its sequence.

`NodeSet` encapsulates a set of nodes in a Graph. NodeSet implements Comparable. There is a method `merge()` for merging two NodeSets.

(These are called "node clusters" in the paper above, but since I've implemented it as an extension of TreeSet, I've used "Set").

`Path` encapsulates a path through a Graph, along with its full sequence in the case of sequence graphs.

### org.ncgr.pangenomics.[allele/genotype].fr

Frequented regions-related code.

`FrequentedRegion` stores a FrequentedRegion, containing a NodeSet along with the supporting subpaths of the full set of Paths in a Graph, and lots of methods.

`FRFinder` contains a `main()` method for finding FRs based on a bunch of parameters.

`FRPair` is a utility class that contains two FRs and the result of merging them, and is used in the search loop in `FRFinder.findFRs()`.

### org.ncgr.svm

LIBSVM-based Support Vector Machine classes.

### org.ncgr.weka

Weka-based supervised classifier classes.