kutils - A collection of kotlin utilities

Installation

To use the library, simply add

compile 'de.mpicbg.scicomp:kutils:0.12'

to the dependencies in your gradle-file.

What's included?

• Fasta and Fastq API (read, write, iterators)
• Parallel collections API
• Bash integration utilities
• IGV session file generator API

Questions & Comments

Feel welcome to flood the isssue tracker with requests.

Examples

Most examples rely on kscript for shell integration

Filter a fasta file with a provided set of ids:

kscript - id.lst some.fasta <<"EOF"
// DEPS de.mpicbg.scicomp:kutils:0.7

import de.mpicbg.scicomp.bioinfo.openFasta
import java.io.File

val filterIds = File(args[0]).readLines()

openFasta(args[1]).
        filter { !filterIds.contains(it.id) }.
        forEach { print(it.toEntryString()) }
EOF

See also

• https://github.com/holgerbrandl/kscript-support-api