Thanks Andy, yea, would be good to add links on the cookbook front page, otherwise the sections are hard to find...
Andreas On Mon, Feb 14, 2011 at 8:13 AM, Andy Yates <[email protected]> wrote: > I've added a bit to the original cookbook page we had. I can migrate these > changes to the cookbook front page later on in the week > > Andy > > On 14 Feb 2011, at 15:42, Andreas Prlic wrote: > > > 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 > > ----------------------------------------------------------------------- > > -- > 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
