[Biojava-dev] Genbank Feature extraction question.

[Richard Holland]

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Hello.

If you are using the BioJavaX parsers as opposed to the older deprecated
ones, then yes, the information is there.

Your parser will be returning instances of RichSequence (there will be a
nextRichSequence or getRichSequence method depending on the way in which
you are using the parser and/or iterator).

Features on a RichSequence are all instances of RichFeature.

Locations for RichFeatures are all instances of RichLocation.

If you cast appropriately (or locate and find the getRich* equivalents
of the get* methods you already using on the non-Rich interfaces) then
you will find that RichLocation does have a getStrand method which will
give you the information you need.

cheers,
Richard

michael walsh wrote:
> BioJava,
> 
> I am writing a program that extracts features from a Genbank file using
> BioJava The program needs to extract the feature locations from the file.
> This is easy enough to do but the location information returned by the
> program does not specify whether or not the location is on the complementary
> strand of DNA.
> 
> This is some of my code:
> FeatureHolder fltrHold = seq.filter(codeFltr);//codeFltr is a filter that
> retrieves coding features only.
>         //iterate over the Features in fh
>         for (Iterator i = fltrHold.features(); i.hasNext(); ){
>             Feature f = (Feature)i.next();
>             System.out.println(f.getLocation().toString());
> 
> An example of the output of the print command is:
> join:[32775..32948,31801..32052]
> 
> However, the entry in the Genbank file reads:
> complement(join(31801..32052,32775..32948))
> 
> Is there any way to get my program to output the fact that a features
> location is on the complementary strand of DNA?
> 
> Any help that anyone can give me would be greatly appreciated.
> 
> Sincerely,
> 
> M Walsh
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev
> 

- --
Richard Holland (BioMart)
EMBL EBI, Wellcome Trust Genome Campus,
Hinxton, Cambridgeshire CB10 1SD, UK
Tel. +44 (0)1223 494416

http://www.biomart.org/
http://www.biojava.org/
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