I have seen 'biojava in anger', but is their a 'biojava cookbook'?
It strikes me that lots of small scripts like this could be useful for
lots of people if archived properly.
Does the cookbook exist?
Cheers, Dan.
On Fri, 5 Mar 2004 [EMAIL PROTECTED] wrote:
> Hi Gera -
>
> The code below seems to work for me. Please note that I have not tested it
> thoroughly so you might want to eyeball a few results to make sure they
> are sensible.
>
> You could probably improve it by making some of the 'in line' code into
> methods etc.
>
> - Mark
>
> import java.io.*;
>
> import org.biojava.bio.*;
> import org.biojava.bio.seq.*;
> import org.biojava.bio.seq.io.*;
> import org.biojava.bio.symbol.*;
>
> /**
> * <p>Program to six-frame translate a nucleotide sequence</p>
> */
>
> public class Hex {
> /**
> * Call this to get usage info, program terminates after call.
> */
> public static void help() {
> System.out.println(
> "usage: java utils.Hex <file> <format eg fasta> <dna|rna>");
> System.exit( -1);
> }
>
> public static void main(String[] args) throws Exception{
> if (args.length != 3) {
> help();
> }
>
> BufferedReader br = null;
> String format = args[1];
> String alpha = args[2];
>
> try {
> br = new BufferedReader(new FileReader(args[0]));
>
> SequenceIterator seqi =
> (SequenceIterator)SeqIOTools.fileToBiojava(format, alpha, br);
>
> //for each sequence
> while(seqi.hasNext()){
> Sequence seq = seqi.nextSequence();
>
> //for each frame
> for (int i = 0; i < 3; i++) {
> SymbolList prot;
> Sequence trans;
>
> //take the reading frame
> SymbolList syms = seq.subList(
> i+1,
> seq.length() - (seq.length() - i)%3);
>
>
> //if it is DNA transcribe it to RNA
> if(syms.getAlphabet() == DNATools.getDNA()){
> syms = RNATools.transcribe(syms);
> }
>
> //output forward translation to STDOUT
> prot = RNATools.translate(syms);
> trans = SequenceTools.createSequence(prot, "",
> seq.getName()+
> "TranslationFrame: +"+i,
> Annotation.EMPTY_ANNOTATION);
> SeqIOTools.writeFasta(System.out, trans);
>
> //output reverse frame translation to STDOUT
> syms = RNATools.reverseComplement(syms);
> prot = RNATools.translate(syms);
> trans = SequenceTools.createSequence(prot, "",
> seq.getName() +
> "TranslationFrame: -" + i,
> Annotation.EMPTY_ANNOTATION);
> SeqIOTools.writeFasta(System.out, trans);
> }
> }
> }
> finally {
> if(br != null){
> br.close();
> }
> }
> }
> }
>
>
>
>
>
> "Jellema, Gera" <[EMAIL PROTECTED]>
> Sent by: [EMAIL PROTECTED]
> 03/04/2004 09:30 PM
>
>
> To: <[EMAIL PROTECTED]>
> cc:
> Subject: [Biojava-l] Reading frames and amino acids
>
>
> Hi,
> I'm new to biojava so I don't know if this has already been asked. I have
> a genome sequence and I want to have it in the 6 reading frames, and then
> per reading frame translated into amino acids so I can look for proteins.
> I don't know how I have to do it.
> Thanks,
> Gera
>
> _______________________________________________
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> http://biojava.org/mailman/listinfo/biojava-l
>
> [ Attachment ''WINMAIL.DAT'' removed by Mark Schreiber ]
>
>
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>
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