To use them add
compile 'de.mpicbg.scicomp:kutils:0.4'
to your dependencies.
- Utilities for kscript
- Fasta and Fastq API (read, write, iterators)
- Parallel collections API
- Bash integration utilities
- IGV session file generator API
Feel welcome to flood the isssue tracker with requests.
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:0.4
import de.mpicbg.scicomp.bioinfo.openFasta
import java.io.File
val filterIds = File(args[0]).readLines()
openFasta(args[1]).
filter { !filterIds.contains(it) }.
forEach { print(it.toEntryString()) }
EOF