Hi,
I want to do something very simple:
- get id and sequence from a database
- create a sequence object
- write it out as fasta format file (with a defined description line)
this is my code:
rs = stmt.executeQuery(query);
Feature.Template templ = new Feature.Template();
//fill in the template
Annotation an = new SimpleAnnotation();
templ.location = Location.empty;
while (rs.next()) {
mepdId = rs.getInt(1);
mepdName = rs.getString(2);
seq = rs.getString(3);
seqObj =
DNATools.createDNASequence(seq, mepdName);
an.setProperty(FastaFormat.PROPERTY_DESCRIPTIONLINE, "my description
here");
templ.annotation = an;
seqObj.createFeature(templ);
SeqIOTools.writeFasta(fastaFos, seqObj);
//db.addSequence(seqObj);
}
It works fine, but there is no description line in the resulting file!
How can I change the fasta description line?
Also I am using deprecated methods, but could not find out what to use
instead:
FastaFormat.PROPERTY_DESCRIPTIONLINE
SeqIOTools.writeFasta
All tutorials I found are using the deprecated.
Cheers,
Thorsten
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