[Biojava-dev] Script for cookbook

[Jolyon Holdstock]

Hi,

 

I was going to add the following script to the annotation section of the
cookbook. 

It takes an EMBL or Genbank file and outputs information about each CDS
feature.

 

I just wanted to check this was OK and also is this the most efficient
way of doing this?

 

Cheers,

 

Jolyon

 

[CODE]

import java.io.*;

import java.util.*;

import org.biojava.bio.*;

import org.biojava.bio.seq.*;

import org.biojava.bio.seq.io.*;

import org.biojavax.*;

import org.biojavax.ontology.*;

import org.biojavax.bio.*;

import org.biojavax.bio.seq.*;

 

public class ExtractInformation {

  //Create the RichSequence object

  RichSequence richSeq;

  public ExtractInformation(String fileName){

    //Load the sequence file

    try {

      richSeq = RichSequence.IOTools.readGenbankDNA(new
BufferedReader(new FileReader(fileName)),null).nextRichSequence();

    }

    catch(FileNotFoundException fnfe){

      System.out.println("FilwNotFoundException: " + fnfe);

    }

    catch(BioException bioe1){

      System.err.println("Not a Genbank sequence trying EMBL");

      try  {

        richSeq = RichSequence.IOTools.readGenbankDNA(new
BufferedReader(new FileReader(fileName)),null).nextRichSequence();

      }

      catch(BioException bioe2){

        System.err.println("Not an EMBL sequence either");

        System.exit(1);

      }

      catch(FileNotFoundException fnfe){

        System.out.println("FilwNotFoundException: " + fnfe);

      }

    }

    //Filter the sequence on CDS features

    FeatureFilter ff = new FeatureFilter.ByType("CDS");

    FeatureHolder fh = richSeq.filter(ff);

 

    //Iterate through the CDS features

    for (Iterator <RichFeature> i = fh.features(); i.hasNext();){

      RichFeature rf = i.next();

      

      //Get the strand orientation of the feature

      char featureStrand = rf.getStrand().getToken();

 

      //Get the location of the feature

      String featureLocation = rf.getLocation().toString();

      

      //Get the annotation of the feature

      RichAnnotation ra = (RichAnnotation)rf.getAnnotation();

 

      //Create the required ComparableTerms

      ComparableTerm geneTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene");

      ComparableTerm locusTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("locus_tag");

      ComparableTerm productTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("product");

      ComparableTerm synonymTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("gene_synonym");

      ComparableTerm proteinIDTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("protein_id");

      

      //Create empty strings

      String gene = "";

      String locus = "";

      String product = "";

      String geneSynonym = "";

      String proteinID = "";

 

      //Iterate through the notes in the annotation 

      for (Iterator <Note> it = ra.getNoteSet().iterator();
it.hasNext();){

        Note note = it.next();

      

      //Check each note to see if it matches one of the required
ComparableTerms

        if(note.getTerm().equals(locusTerm)){

          locus = note.getValue().toString();

        }

        if(note.getTerm().equals(productTerm)){

          product = note.getValue().toString();

        }

        if(note.getTerm().equals(geneTerm)){

          gene = note.getValue().toString();

        }

        if(note.getTerm().equals(synonymTerm)){

          geneSynonym = note.getValue().toString();

        }

        if(note.getTerm().equals(proteinIDTerm)){

          proteinID = note.getValue().toString();

        }

      }

      //Outout the feature information

      System.out.println(locus + "  " + gene + "  " + geneSynonym + "  "
+ proteinID + "  " + product +"  " + featureStrand +"  Chr1:" +
featureLocation);

    }

  }

 

  public static void main(String args []){

    if (args.length != 1){

      System.out.println("Usage: java ExtractInformation <file in
Genbank or EMBL format>");

      System.exit(1);

    }

    else {

      new ExtractInformation(args[0]);

    }

  }

}

[/CODE]

 

Dr. Jolyon Holdstock                                       
Senior Computational Biologist,

Oxford Gene Technology,                                   
Begbroke Science Park,                                     
Sandy Lane, Yarnton,                                           
Oxford, OX5 1PF, UK.                                             

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