[Biojava-l] Parsing Genbank-sequences from NCBI

Fri Jul 14 08:56:11 UTC 2006

This exception happens whenever the Genbank record has a reference that
either does not have any author or consortium tags, or has no location.

Are you sure you're using the latest version from CVS? The code I've got
here works just fine and it's the same as what's in CVS.

cheers,
Richard

On Thu, 2006-07-13 at 20:46 +0200, Felix Dreher wrote:
> Hello,
> 
> I have a problem with the parsing of Genbank-Sequences from NCBI.
> 
> The probably most important line of the log (see below) is the following:
> Error while trying to call new class org.biojavax.SimpleDocRef(class 
> java.util.ArrayList,class java.lang.String,class java.lang.String)
> 
> This exception is thrown when I run the following code (with the latest 
> CVS version):
> 
>         GenbankRichSequenceDB  ncbi = new GenbankRichSequenceDB();
>         ncbi.setNamespace(RNAiDBFactory.getTargetDBNamespace());
>         RichSequence rs = ncbi.getRichSequence("110002612");
> 
> 
> If I use the CVS version of March 2006, a different exception is thrown. 
> This is said to be fixed
> (Re: [Biojava-l] Parsing Genbank/EMBL/XML Sequences from binary NCBI 
> ASN.1 daily update files
>  Richard Holland
> Fri, 02 Jun 2006 02:16:07 -0700)
> 
> 
> 
> Any help would be highly appreciated!
> Best regards,
> Felix
> 
> 
> 
> current exception:
> 
> 2006-07-13 20:28:04,446 ERROR [main]
> Error:
> org.biojava.bio.BioException: Failed to read Genbank sequence
>     at 
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:157)
>     at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237)
>     at rnaiserver.calculation.TestRun.main(TestRun.java:40)
> Caused by: org.biojava.bio.BioException: Could not read sequence
>     at 
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
>     at 
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:153)
>     ... 2 more
> Caused by: java.lang.RuntimeException: Error while trying to call new 
> class org.biojavax.SimpleDocRef(class java.util.ArrayList,class 
> java.lang.String,class java.lang.String)
>     at 
> org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:156)
>     at org.biojavax.RichObjectFactory.getObject(RichObjectFactory.java:104)
>     at 
> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:385)
>     at 
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
>     ... 3 more
> Caused by: java.lang.reflect.InvocationTargetException
>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>     at 
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>     at 
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>     at java.lang.reflect.Method.invoke(Method.java:585)
>     at 
> org.biojavax.bio.db.biosql.BioSQLRichObjectBuilder.buildObject(BioSQLRichObjectBuilder.java:123)
>     ... 6 more
> Caused by: org.hibernate.exception.GenericJDBCException: could not 
> execute query
>     at 
> org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:91)
>     at 
> org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:79)
>     at 
> org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
>     at org.hibernate.loader.Loader.doList(Loader.java:2148)
>     at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2029)
>     at org.hibernate.loader.Loader.list(Loader.java:2024)
>     at org.hibernate.loader.hql.QueryLoader.list(QueryLoader.java:375)
>     at 
> org.hibernate.hql.ast.QueryTranslatorImpl.list(QueryTranslatorImpl.java:308)
>     at 
> org.hibernate.engine.query.HQLQueryPlan.performList(HQLQueryPlan.java:153)
>     at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1129)
>     at org.hibernate.impl.QueryImpl.list(QueryImpl.java:79)
>     at 
> org.hibernate.impl.AbstractQueryImpl.uniqueResult(AbstractQueryImpl.java:749)
>     ... 11 more
> Caused by: org.postgresql.util.PSQLException: ERROR: current transaction 
> is aborted, commands ignored until end of transaction block
>     at 
> org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1512)
>     at 
> org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1297)
>     at 
> org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:188)
>     at 
> org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:437)
>     at 
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:353)
>     at 
> org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:257)
>     at 
> org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:139)
>     at org.hibernate.loader.Loader.getResultSet(Loader.java:1669)
>     at org.hibernate.loader.Loader.doQuery(Loader.java:662)
>     at 
> org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:224)
>     at org.hibernate.loader.Loader.doList(Loader.java:2145)
>     ... 19 more
> 
> 
> 
> 
> 
> 
> 'old' exception with Biojava-live from March 2006:
> 
> 2006-07-13 20:22:08,425 ERROR [main]
> Error:
> org.biojava.bio.BioException: Failed to read Genbank sequence
>     at 
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:156)
>     at rnaiserver.calculation.TestRun.downloadSequences(TestRun.java:237)
>     at rnaiserver.calculation.TestRun.main(TestRun.java:40)
> Caused by: org.biojava.bio.BioException: Could not read sequence
>     at 
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111)
>     at 
> org.biojavax.bio.db.ncbi.GenbankRichSequenceDB.getRichSequence(GenbankRichSequenceDB.java:152)
>     ... 2 more
> Caused by: java.lang.IllegalArgumentException: Authors string cannot be null
>     at 
> org.biojavax.DocRefAuthor$Tools.parseAuthorString(DocRefAuthor.java:75)
>     at 
> org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:323)
>     at 
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108)
>     ... 3 more
> _______________________________________________
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416