Hi all,
I have a BioSQL database which contains all human chromosomes. My
intention is to get the information about a particular gene. How can I
get a part of a particular chromosome with all associated features? At
the moment I use following code to create my new sequence:
<code>
RichSequence subSeq = RichSequence.Tools.subSequence(parent,
position[0], position[1], ns, geneName, parent.getAccession(),
parent.getIdentifier(), parent.getVersion() + 1,
(Double) (parent.getVersion() + 1.0));
<\code>
Here is the part how I get the parent sequence:
<code>
public static RichSequence getChromosome(String chrNo) {
Transaction tx = session.beginTransaction();
RichSequence ret = null;
String query;
try {
if (chrNo.equals("MT")) {
query = "from BioEntry as be where be.description
like '%:num%'";
query = query.replaceAll(":num",
"mitochondrion");
} else {
query = "from BioEntry as be where be.description like '%hromosome
:num%'";
query = query.replaceAll(":num", chrNo);
}
Query q = session.createQuery(query);
ret = (RichSequence) q.list().get(0);
tx.commit();
} catch (Exception e) {
tx.rollback();
e.printStackTrace();
}
return ret;
}
<\code>
I always have to load the whole chromsome to get a part of it, so it
takes very long time and I get a lot of unused information (waste of
memory). I also tried to use <code>ThinRichSequence<\code> instead of
<code>RichSequence<\code>, but thereby I didn't notice any difference.
Can you give me a hint how to accelerate the code?
I am grateful for any hits.
cheers,
Gabrielle
_______________________________________________
Biojava-l mailing list - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
