[Bioperl-l] Bio:DB:SeqFeature - MySql - Java
bernd.jagla at pasteur.fr
Mon Jan 11 05:11:16 EST 2010
First off, I am not sure if this is supposed to be addressed to the Bioperl
or Gbrowse mailing list, so apologies if this is the wrong list and please
let me know.
I am writing a program in Java that needs to access genome annotation data.
Since I am using Gbrowse already I was thinking that I could combine both
approaches making life eventually easier for me. I am mainly interested in
getting a gene/feature name for a given position. The position is stored in
the feature table and through linking typelist, locationlist, (maybe
sequence), and feature I can get all the information I need. Unfortunately
it seems that the feature name is stored in the object blog of the feature
That is a bit suspicious to me because I don't understand why searching for
a name can be so fast if it is not indexed through mysql when searching
So my question is how to I parse the Bio::DB::SeqFeature object in JAVA
correctly to get the name of the feature and possible also any further
Any suggestions are greatly appreciated. Maybe there is a better solution
than parsing Perl code with Java.?
Thanks a lot,
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