Hi Andy, Could we get a Cookbook page for this? sounds like it would be good to have a bit more docu on this topic ...
Thanks! Andreas On Mon, Feb 14, 2011 at 2:07 AM, Andy Yates <[email protected]> wrote: > If you want to do frame based translation then there is an easier way of > accomplishing this. The TranscriptionEngine allows you to translate in > multiple frames and retrieve that information in a Map such as: > > TranscriptionEngine te = TranscriptionEngine.getDefault(); > Frame[] frames = Frame.getForwardFrames(); > Map<Frame, Sequence<AminoAcidCompound>> results = > te.multipleFrameTranslation(dna, frames); > > Change the static call on Frame to Frame.getAllFrames() then you will do a > full 6 frame translation. > > Also I would avoid calling the getSequenceAsString() method until you need > to output it to screen. The Sequence interface provides an adequate set of > methods for testing length of a sequence. However if you want is the longest > translation then I would replace that with (assuming the above code): > > List<Sequence<AminoAcidCompound>> translations = new > ArrayList<Sequence<AminoAcidCompound>>(results.getValues()); > Collections.sort(translations, new > Comparator<Sequence<AminoAcidCompound>>() { > public int compare(Sequence<AminoAcidCompound> o1, > Sequence<AminoAcidCompound> o2) { > Integer o1Length = o1.getLength(); > Integer o2Length = o2.getLength(); > return o1Length.compareTo(o2Length); > } > }); > Sequence<AminoAcidCompound> longest = > translations.get(translations.size()-1); > > However I would like to see what errors you are pulling up from BioJava3 in > case there is a scenario we are not currently taking into account > > Andy > > On 14 Feb 2011, at 02:27, Shamanou van Leeuwen wrote: > > > On 13-02-11 20:11, Scooter Willis wrote: > >> Depending on what you need you may want to try out biojava3. > >> > >> On Sun, Feb 13, 2011 at 9:32 AM, Shamanou van Leeuwen > >> <[email protected]> wrote: > >>> hi guys, > >>> > >>> i made am making a tool to translate dna to protein using biojava. > >>> But i am getting some errors that is do not fully understand. > >>> Can somebody please tell me what i am doing wrong? > >>> > >>> > >>> script: > >>> http://pastebin.com/TJSjkgqK > >>> > >>> errors: > >>> http://pastebin.com/iFXYWEZB > >>> _______________________________________________ > >>> Biojava-l mailing list - [email protected] > >>> http://lists.open-bio.org/mailman/listinfo/biojava-l > >>> > >>> > > i a, trying biojava 3 now but i am still doing something wrong. > > > > http://pastebin.com/uLz934gr > > _______________________________________________ > > Biojava-l mailing list - [email protected] > > http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- > Andrew Yates Ensembl Genomes Engineer > EMBL-EBI Tel: +44-(0)1223-492538 > Wellcome Trust Genome Campus Fax: +44-(0)1223-494468 > Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/ > > > > > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -- ----------------------------------------------------------------------- Dr. Andreas Prlic Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego (+1) 858.246.0526 ----------------------------------------------------------------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
