[Biojava-l] BioJava translation

[Pjotr Prins]

On Wed, Oct 13, 2010 at 12:27:05PM +0100, Richard Holland wrote:
> BJ3 should be replacing most sequence operations with string operations, making the whole thing much faster.

Good news, BJ3 is a lot faster! The previous version took 2 minutes
for the C.elegans genome (33 Mb), the BJ3 version takes 27sec on my
modest Thinkpad X61 laptop. After parsing the Fasta and turning it
into an upper case string the actual translation takes 16sec.

Only the C implementations are faster.

Here the relevant Scala code:

import bio._
import java.io._
import org.biojava3.core.sequence._
import org.biojava3.core.sequence.transcription.TranscriptionEngine
import org.biojava3.core.sequence.io.IUPACParser

// <cut> fetching infile from command line...

IUPACParser.getInstance().getTable(1);  // not sure we need this
IUPACParser.getInstance().getTable("UNIVERSAL");
val engine = TranscriptionEngine.getDefault()
val f = new FastaReader(infile)
f.foreach { 
  res => 
    val (id,tag,dna) = res
    println(List(">",id).mkString) 
    val dna2 = new DNASequence(dna.mkString.toUpperCase)
    val rna = dna2.getRNASequence(engine)
    println(rna.getProteinSequence(engine))
  }
}

prints:

>B0222.10
MLYWNDLNTVGIVADTIWKYYADQYKRLIKEHSKIRFNPLLHAASVIRIFDIHINLFNNFVTFLLVIFLYIFLIYYVTFFVFPFGPLRVSHWMRFFKIIISRSHLG
>B0222.11
MSRRTASKLLVFVFLCSLCFGTQRYDMPRKIDLFNDLITQSTTPASPKCQCLPPTTPSTPPNCIPYDSRLQAASLEEAIVAFPDLTITRQEKTQQSTATLNNCKTKQCRDCYKDLRSQLRKVGLLPGTIDQVFHNQRNFTTCQKYRFARQDKGVYEKKKKAKQHYDWDYVEYDEDEDDDYFWDGLFWKKKRNVLKKIVKRDVEATTAISQPPNSTAMNSTGIIGIRFPISCTTRGVTPDGLGTVSLCSTCWVWRRLPSTYYPAYLNEVVCDYADTSCLSGYASCQTGTQQLNVLRNDSGKLIPISVSAGINCECRLAVGSTLESLVLGQGISKAMPPIDTTSTKPPNLATSTTSHS
(...)

Pj.