[Biojava-dev] RichSequence.Tools.enrich(..) generateNoSuchElementException

[Richard HOLLAND]

Hello all.

There was indeed a bug (in the constructor of SimpleRichFeature) which
is now fixed, but Mark is right about using the appropriate BioJavaX
parser instead to do this task.

I've added a new module in biojava-live in CVS -
org.biojavax.bio.seq.db.ncbi.GenbankSequenceDB. See the
getRichSequence(), getRichSequenceDB() and getRichSequences() methods
for details.

Your sample code will work with the new module after you do this:

	1. 	Import org.biojavax.bio.seq.db.ncbi.GenbankSequenceDB
instead of org.biojava.bio.seq.db.GenbankSequenceDB
	2. 	change
			Sequence seq = sequenceIterator.nextSequence();
		to
			RichSequence seq =
(RichSequence)sequenceIterator.nextSequence();
	3. 	delete the line that calls enrich().

(Note: GenbankSequenceDB should probably be tidied up a little and made
to implement some kind of common interface, maybe RichSequenceDB?
Comments please.)

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: mark.schreiber at novartis.com 
> [mailto:mark.schreiber at novartis.com] 
> Sent: Monday, January 23, 2006 10:03 AM
> To: Janko Diminic
> Cc: biojava-dev at biojava.org; Richard HOLLAND
> Subject: Re: [Biojava-dev] RichSequence.Tools.enrich(..) 
> generateNoSuchElementException
> 
> 
> Hi -
> 
> Will have a look into this.
> 
> However, the enrich method is not the ideal way to do this. 
> The method 
> will do it's best to make a Sequence into a RichSequence but 
> it usually 
> cannot do a great job. Your best bet would be to use NCBI 
> eutils to get 
> sequences in GenBank or XML and then put them through the appropriate 
> parser to directly generate a RichSequence.
> 
> As a todo, we should update GenbankSequenceDB to provide RichSequence 
> instances (or deprecate it and provide an alternative).
> 
> - Mark
> 
> 
> 
> 
> 
> Janko Diminic <jdiminic at gmail.com>
> Sent by: biojava-dev-bounces at portal.open-bio.org
> 01/21/2006 02:52 PM
> 
>  
>         To:     biojava-dev at biojava.org
>         cc:     (bcc: Mark Schreiber/GP/Novartis)
>         Subject:        [Biojava-dev] 
> RichSequence.Tools.enrich(..) generate 
> NoSuchElementException
> 
> 
> Hi, RichSequence.Tools.enrich(seq) generate NoSuchElementException 
> exception:
> 
> // Samples.java class
> 
>     Set param = new HashSet();
>     param.add("AJ278573");   // NCBI accession
> 
>     GenbankSequenceDB genBank = new GenbankSequenceDB();
>     SequenceDB sequences = genBank.getSequences(param);
> 
>     sequenceIterator = sequences.sequenceIterator();
> 
> while (sequenceIterator.hasNext()) {
>         try {
>               Sequence seq = sequenceIterator.nextSequence();
>               RichSequence enrichSeq = RichSequence.Tools.enrich(seq);
>   //line:92,  here throw NoSuchElementException ???
> 
>               session.saveOrUpdate("Sequence", enrichSeq);
> 
>               } catch (NoSuchElementException e) {
>                      e.printStackTrace();
>               }
>         }
> 
> 
> 
> java.util.NoSuchElementException
>     at 
> java.util.LinkedHashMap$LinkedHashIterator.nextEntry(LinkedHas
hMap.java:367)
>     at 
> java.util.LinkedHashMap$KeyIterator.next(LinkedHashMap.java:376)
>     at 
> org.biojavax.bio.seq.SimpleRichFeature.<init>(SimpleRichFeatur
> e.java:96)
>     at 
> org.biojavax.bio.seq.SimpleRichSequence.createFeature(SimpleRi
> chSequence.java:323)
>     at 
> org.biojavax.bio.seq.RichSequence$Tools.enrich(RichSequence.java:434)
>     at hr.Samples.main(Samples.java:92)
> 
> 
> Do you know way?
> Thanks for the help.
> 
> 
> 
> --
> Janko Diminic
> 
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> 
> 
> 
>