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https://github.com/jetbrains-research/big
BigWIG, BigBED and TDF for the JVM
https://github.com/jetbrains-research/big
bigbed bigwig jvm kotlin tdf
Last synced: about 1 month ago
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BigWIG, BigBED and TDF for the JVM
- Host: GitHub
- URL: https://github.com/jetbrains-research/big
- Owner: JetBrains-Research
- License: mit
- Created: 2015-02-16T17:33:54.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2021-02-23T12:20:18.000Z (almost 4 years ago)
- Last Synced: 2023-07-28T18:20:19.175Z (over 1 year ago)
- Topics: bigbed, bigwig, jvm, kotlin, tdf
- Language: Kotlin
- Homepage:
- Size: 21.7 MB
- Stars: 12
- Watchers: 12
- Forks: 2
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES
- License: LICENSE
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# big
`big` implements high performance classes for reading and writing BigWIG,
BigBED and TDF. You can use `big` in any programming language running on the
JVM, but the public API is in part Kotlin-specific.
Installation
------------
The latest version of `big` is available on [Maven Central] [maven-central]. If you're using
Gradle just add the following to your `build.gradle`:
```groovy
repositories {
mavenCentral()
}
dependencies {
compile 'org.jetbrains.bio:big:0.9.1'
}
```
With Maven, specify the following in your `pom.xml`:
```xml
org.jetbrains.bio
big
0.9.1
```
The previous versions were published on Bintray. They can be downloaded
from [GitHub Releases](https://github.com/JetBrains-Research/big/releases).
[maven-central]: https://search.maven.org/artifact/org.jetbrains.bio/big/0.9.1/jar
Examples
--------
The following examples assume that all required symbols are imported into the
current scope. They also rely on the helper function for reading TSV formated
[chromosome sizes] [chrom-sizes] from UCSC annotations.
```kotlin
/** Fetches chromosome sizes from a UCSC provided TSV file. */
internal fun Path.chromosomes(): List> {
return Files.newBufferedReader(this).lineSequence().map { line ->
val chunks = line.split('\t', limit = 3)
chunks[0] to chunks[1].toInt()
}.toList()
}
```
### wigToBigWig
```kotlin
fun wigToBigWig(inputPath: Path, outputPath: Path, chromSizesPath: Path) {
BigWigFile.write(WigFile(inputPath), chromSizesPath.chromosomes(), outputPath)
}
```
### bigWigSummary
```kotlin
fun bigWigSummary(inputPath: Path, numBins: Int) {
BigWigFile.read(inputPath).use { bwf ->
println("Total: ${bwf.totalSummary}")
for (chromosome in bwf.chromosomes.valueCollection()) {
for ((i, summary) in bwf.summarize(chromosome, numBins = numBins).withIndex()) {
println("bin #${i + 1}: $summary")
}
}
}
}
```
### bedToBigBed
```kotlin
fun bedToBigBed(inputPath: Path, outputPath: Path, chromSizesPath: Path) {
BigBedFile.write(BedFile(inputPath), chromSizesPath.chromosomes(), outputPath)
}
```
### bigBedToBed
```kotlin
fun bigBedToBed(inputPath: Path) {
BigBedFile.read(inputPath).use { bbf ->
for (chromosome in bbf.chromosomes.valueCollection()) {
for ((chrom, start, end) in bbf.query(chromosome)) {
// See 'BedEntry' for a complete list of available
// attributes.
println("$chrom\t$start\t$end")
}
}
}
}
```
[chrom-sizes]: http://genome.ucsc.edu/goldenpath/help/hg19.chrom.sizes
Building from source
--------------------
The build process is as simple as
```bash
$ ./gradlew jar
```
Note: don't use `./gradlew assemble`, since it includes the signing of the artifacts
and will fail if the correct credentials are not provided.
Testing
-------
No extra configuration is required for running the tests from Gradle
```bash
$ ./gradlew test
```
Publishing
----------
You can publish a new release with a one-liner
```bash
./gradlew clean assemble test generatePomFileForMavenJavaPublication bintrayUpload
```
Make sure to set Bintray credentials (see API key section
[here](https://bintray.com/profile/edit)) in `$HOME/.gradle/gradle.properties`.
```
$ cat $HOME/.gradle/gradle.properties
bintrayUser=CHANGEME
bintrayKey=CHANGEME
```
Useful links
------------
* Kent et al. [paper] [paper] in Bioinformatics
* UCSC documentation on [WIG] [wig], [BED] [bed], [BigWIG] [bigwig] and [BigBED] [bigbed]
* Reference C [implementation](http://hgdownload.cse.ucsc.edu/admin/exe) of both
big formats by UCSC
* Sketch of [TDF spec.] [tdf] in IGV repository and another version [on Gist] [tdf-gist]
[paper]: http://bioinformatics.oxfordjournals.org/content/26/17/2204.abstract
[wig]: http://genome.ucsc.edu/goldenpath/help/wiggle.html
[bed]: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
[bigwig]: http://genome.ucsc.edu/goldenpath/help/bigWig.html
[bigbed]: http://genome.ucsc.edu/goldenpath/help/bigBed.html
[tdf]: https://github.com/igvteam/igv/blob/master/src/org/broad/igv/tdf/notes.txt
[tdf-gist]: https://gist.github.com/superbobry/c67614cbfe2a15d35d5c