[Biojava-dev] Script for cookbook
Alessandro Cipriani
genjasp at gmail.com
Wed Jan 13 14:14:26 UTC 2010
Hi,
i think it is not a good practice:
-to insert a try/catch block into anothet try/catch block.
-to import all lib even unrequired
-to make all methods public
otherwise it seems to be ok!
Regards
Alex
2010/1/13 Richard Holland <holland at eaglegenomics.com>:
> Just a few minor points, otherwise all good:
>
> 1. Your 'trying EMBL' code just tries Genbank again!
> 2. Typo in the FileNotFoundException message.
> 3. Check to see that your ComparableTerm retrieval statements using RichObjectFactory are not already defined as constants in RichSequence.Terms or GenbankFormat.Terms. If they are, use the constants instead as this makes the code clearer.
> 4. Your system.out line that prints the results has Chr1 hardcoded - should this be a parameter, or read from the file maybe?
>
> cheers,
> Richard
>
> On 13 Jan 2010, at 12:49, Jolyon Holdstock wrote:
>
>> 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.
>>
>> T: +44 (0)1865 856 852
>> F: +44 (0)1865 842 116
>> E: jolyon.holdstock at ogt.co.uk <mailto:nicola.booton-mander at ogt.co.uk>
>>
>> W: www.ogt.co.uk <blocked::http://www.ogt.co.uk/>
>>
>>
>>
>> Looking to outsource your microarray studies? Look no further.
>> Click here to tour our facilities
>> <http://www.ogt.co.uk/highthroughputservices.html>
>>
>> Click here to request a quotation
>> <http://www.ogt.co.uk/htsquotationrequest.asp>
>>
>>
>>
>> Scientific pedigree delivering high quality microarray results to you:
>>
>> * Service capacity >1000 samples per week
>>
>> * Rigorous QC <http://www.ogt.co.uk/hts_qc.html> from sample to
>> result
>>
>> * Applications <http://www.ogt.co.uk/hts_apps.html> available
>> include aCGH, CNV, methylation studies and miRNA
>>
>>
>>
>> Oxford Gene Technology (Operations) Ltd. Registered in England No:
>> 03845432 Begbroke Science Park Sandy Lane Yarnton Oxford OX5 1PF
>>
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>>
>>
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>
> --
> Richard Holland, BSc MBCS
> Operations and Delivery Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
>
>
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