My preference would be to leave the existing method as-is, and modify the
javadocs so that it is explicit that it is searching by name and not accession.
This is to prevent breaking any code that may rely on this behaviour (as
Genbank is not the only kind of sequence that can be stored in BioSQL, we can't
guarantee that other sequence types are not using name as the unique identifier
instead).
Instead, I would propose adding a second method called
getRichSequencesByAccession, with the modification you suggest.
With regard to your last point about bad section errors, could you post the
stack trace and the code that causes it?
cheers,
Richard
On 11 Feb 2010, at 22:00, Deepak Sheoran wrote:
> Hi
> This class(BiosqlRichSequence) have methods to retrieve record from a local
> instance of biosql schema but when you type in accession number for record it
> mostly show the info but in some case (Record with accession:M97762) it give
> following error :
>
> Hibernate: select sequence0_.bioentry_id as bioentry1_9_,
> sequence0_1_.name as name9_, sequence0_1_.identifier as identifier9_,
> sequence0_1_.accession as accession9_, sequence0_1_.description as
> descript5_9_, sequence0_1_.version as version9_, sequence0_1_.division as
> division9_, sequence0_1_.taxon_id as taxon8_9_, sequence0_1_.biodatabase_id
> as biodatab9_9_, sequence0_.version as version13_, sequence0_.length as
> length13_, sequence0_.alphabet as alphabet13_, sequence0_.seq as seq13_ from
> biosequence sequence0_ inner join bioentry sequence0_1_ on
> sequence0_.bioentry_id=sequence0_1_.bioentry_id where sequence0_1_.name=?
> Exception in thread "main" java.lang.RuntimeException: Error while trying to
> load by id: M97762
> at
> org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:212)
> at
> com.orionbiosciences.orionGenBankLib.genBankDb.GenBankDb.GenBankDbToFileDownLoader(GenBankDb.java:355)
> at trashtesting.Main.main(Main.java:39)
> Caused by: org.biojava.bio.seq.db.IllegalIDException: Id not found: M97762
> at
> org.biojavax.bio.db.biosql.BioSQLRichSequenceDB.getRichSequence(BioSQLRichSequenceDB.java:206)
> ... 2 more
> Java Result: 1
>
> The only way to find this record in my database is to search for LOCUS
> instead of Accession number which is "BTVNS1TUBA", java doc for
> BioSqlRichSequenceDb class say the id should be Genbank Id i can't
> understand what does that means, but when investigated the matter the error
> is in following method
>
> public RichSequenceDB getRichSequences(Set ids, RichSequenceDB db) throws
> BioException, IllegalIDException {
> if (db==null) db = new HashRichSequenceDB();
> try {
> for (Iterator i = ids.iterator(); i.hasNext(); ) {
> String id = (String)i.next();
> // Build the query object
> ***************************error*******************
> String queryText = "from Sequence where name = ?";
> ***************************error***********************
> *****************************solution**************************
> String queryText = "from Sequence where accession = ?";
> // because name stand for Locus from gen-bank record which
> don't have any unique constraint name so its should not be good idea to use
> it for searching unique records
> // also people usually refer to a gen-bank record using
> accession number instead of LOCUS
> *****************************solution******************************
> Object query = this.createQuery.invoke(this.session, new
> Object[]{queryText});
> // Set the parameters
> query = this.setParameter.invoke(query, new Object[]{new
> Integer(0), id});
> // Get the results
> List result = (List)this.list.invoke(query,(Object[]) null);
> // If the result doesn't just have a single entry, throw an
> exception
> if (result.size()==0) throw new IllegalIDException("Id not
> found: "+id);
> // Add the results to the results db.
> for (Iterator j = result.iterator(); j.hasNext(); )
> db.addRichSequence((RichSequence)j.next());
> }
> } catch (Exception e) {
> // Throw the exception with our nice message
> throw new RuntimeException("Error while trying to load by ids:
> "+ids,e);
> }
> return db;
> }
>
> even ncbi says " It is better to search for the actual accession number
> rather than the locus name, because the accessions are stable and locus names
> can change."
> REF: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#LocusNameB
>
> So my suggestion is to change the query so it will look for accession instead
> of name in this method.
> Also if you will try to download record from ncbi using java interface first
> with accession:M97762( as genbank_id) you can get it, but when you try to get
> using LOCUS you will get bad section exception around reference I don't
> know why ?
>
>
> Deepak Sheoran
>
>
>
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--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: [email protected]
http://www.eaglegenomics.com/
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