[Biojava-l] How to extract chromosome ID from a Transcript?

[Alberto Ambesi]

Thank you for your help!
	Now I have another problem, on the same code. Apparently, the iterator 
on 'transcripts' extracts multiple copies of same features, if the gene 
has more than one transcript. I just can't figure why. I adjusted my 
code in order to skip redundancies, but is there a more elegant way?
	Thank you,
dr Alberto Ambesi.


On Friday, July 4, 2003, at 06:23 PM, Thomas Down wrote:

> Once upon a time, Alberto Ambesi wrote:
>> I can successfully extract Location and Strand features from a
>> transcript, but I can't find a way to get the chromosome ID where the
>> gene is located. I am using the following code:
>>
>>         SequenceDB chromosomes =ens.getChromosomes();
>>         FeatureHolder transcripts = chromosomes.filter(
>>             new FeatureFilter.ByAnnotation(Ensembl.TRANSCRIPT_GENEID,
>> ensID)
>>         );
>>         iter= transcripts.features();
>>         while (iter.hasNext()) {
>>             StrandedFeature feat = (StrandedFeature)iter.next();
>>             System.out.println("Strand: \t" +
>> feat.getStrand().toString());
>>             System.out.println("Location: \t" + feat.getLocation());
>>         }
>
> All BioJava Features `know' their sequence.  In this case, you
> should just be able to use:
>
>      feat.getSequence().getName()
>
> Hope this helps,
>
>     Thomas.
>