Hi Hedwig,
The problem holds with StrandedFeature. The strandeness of a feature
is the transdeness of its location. StrandedFeature should be
eliminated from bj1. Use biojavaX instead, something like this, once
you have created a RichLocation on the appropriate strand:
public Feature.Template getFeatureTemplate(RichSequence
parent,RichLocation loc) {
RichFeature.Template templ = new RichFeature.Template();
RichAnnotation rans = new SimpleRichAnnotation();
templ.annotation = rans;
templ.sourceTerm = // find an appropriate term
templ.typeTerm =
RichObjectFactory.getDefaultOntology().getOrCreateTerm("CDS");
templ.featureRelationshipSet = new TreeSet();
templ.rankedCrossRefs = new TreeSet();
templ.location = loc;
// add notes if any you'd like
return templ;
}
That should make it into the output file.
Regards,
George
Quoting Hedwig Kurka <[email protected]>:
Hello all,
I have a problem concerning creating EMBL or Genbank files.
Below is a fragment of my code and an example of how the EMBL file looks
like.
String name = "test genome";
String seqString = pFasta.getSequence(1, pFasta.getLength());
Sequence seq = DNATools.createDNASequence(seqString, name);
Alphabet dna = AlphabetManager.alphabetForName("DNA");
RichSequence rs =
Tools.createRichSequence(RichObjectFactory.getDefaultNamespace(), name,
seqString, dna);
Set<Feature> rfeatSet = new HashSet<Feature>();
StrandedFeature.Template t = new StrandedFeature.Template();
for(int i=0; i<annotierten.size(); i++){
int start = (int) Math.abs(anno.get(i).getStart());
int stop = (int) Math.abs(anno.get(i).getStop());
t.type = "CDS";
if(start < stop){
t.location = new RangeLocation(start, stop);
t.strand = StrandedFeature.POSITIVE;
}
if(start > stop){
t.location = new RangeLocation(stop, start);
t.strand = StrandedFeature.NEGATIVE;
}
Feature f = seq.createFeature(t);
RichFeature rf = RichFeature.Tools.enrich(f);
rfeatSet.add(rf);
}
rs.setFeatureSet(rfeatSet);
rs = RichSequence.Tools.enrich(rs);
RichSequence.IOTools.writeEMBL(output, rs,
RichObjectFactory.getDefaultNamespace());
EMBL file:
FT any 1889536..1890903
FT any 134636..136987
FT any 3727110..3727625
FT any 2812636..2813517
FT any 580648..581643
FT any 2330962..2331921
FT any 1012371..1013513
FT any 1260854..1261720
FT any 1602858..1603706
FT any 4108079..4108999
FT any 346637..347731
FT any 4073395..4074549
I wonder where the information of plus and minus strand is, why is there
"any" in the file and not "CDS" and so on.
As tutorial I found that:
http://www.biojava.org/wiki/BioJava:Cookbook:Locations:Feature. Is there
another one?
Thank you for your help!
And any help is appreciated,
Hedwig
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