[Biojava-l] Reading frames and amino acids

[mark.schreiber at group.novartis.com]

That is the intention of the 'biojava in anger' site. I just haven't had 
time to add lots of little scripts to it. I will gratefully take 
donations.

- Mark






Dan Bolser <dmb at mrc-dunn.cam.ac.uk>
03/05/2004 05:29 PM

 
        To:     Mark Schreiber/GP/Novartis at PH
        cc:     "Jellema, Gera" <Gera.Jellema at wur.nl>, biojava-l at portal.open-bio.org, 
biojava-l-bounces at portal.open-bio.org
        Subject:        Re: [Biojava-l] Reading frames and amino acids




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 mark.schreiber at group.novartis.com 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" <Gera.Jellema at wur.nl>
> Sent by: biojava-l-bounces at portal.open-bio.org
> 03/04/2004 09:30 PM
> 
> 
>         To:     <biojava-l at portal.open-bio.org>
>         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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> 
> [ Attachment ''WINMAIL.DAT'' removed by Mark Schreiber ]
> 
> 
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