BioKotlin

Kotlin programming language realisation of bioinformatics routine operations and file handling. FASTA, FASTQ and GFF basics are available.

Now You can use following commands as: java -jar bioKotlin.jar <command> <command arguments>

GenomeStats - output statistics (N50, GC etc.) for Fasta file.
TetraStats - output tetranucleotide composition for each contig for Fasta file.
AlignmentStats - output statistics for Fasta alignment.
AlignmentClearGaps <0-100> - treshold gap share to remove column from alignment. Integer value, columns containng less than this value still in the alignment.
FastaToSeqPhylip [nostrict] - convert Fasta alignment sequental Phylip format. It may produce duplicated IDs in strict mode. Some software can use only strict Phylip format (like PHYLIP programs), while other (e.g. FastME) may use "non-strict" alignments.
FastqPairing - check files for orphaned reads and write sorted.
FilterShortSeqsFasta - filter out short sequences FASTA.
FilterShortSeqsFastq - filter out short sequences FASTQ.

Data will be printed to standard output.

To see a short help message just run without any commands and arguments: java -jar bioKotlin.jar

Compilation

Use Gradle to build the project:

gradle jar

Run gradle test to perform few unit tests. Hopefully we'll have more in the future.

Read FASTA (uncompressed, gzip, bzip2) and FASTQ (uncompressed, gzip and bzip2) from files.
Get any locus of sequence from FASTA file without prior indexing (reverse complement if start > end).
Filter sequences by length.
Genome statistics from FASTA: N50, L50, N90, L90, GC(%), N's.
GFF parsing.
NCBI BLASTn results parsing for JSON (-outfmt 15).
Tetranucleotide composition statistics.
Removing orphan reads from paired-end FASTQ files (memory unefficient, but working).