Hi and thanks for for the reply,
I have reloaded the biosql-db schema to mysql and I have inserted one sequence form a
Genbank format with the 'load_seqdatabase.pl' perl script.
When I try to fetch this entry for the first time with Biojava1.4pre1 I get this error
:
---------------------------------------------------------------------------------
*** Importing a core ontology -- hope this is okay
*** Importing terms
org.biojava.bio.BioException: Error accessing ontologies
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:238)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.<init>(BioSQLSequenceDB.java:193)
at ca.warnex.sab.util.helpers.biosqlTest.main(biosqlTest.java:49)
Caused by: java.sql.SQLException: General error, message from server: "Table
'bioseqdb.term_relationship_term' doesn't exist"
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:1977)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1163)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1272)
at com.mysql.jdbc.Connection.execSQL(Connection.java:2236)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1741)
at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1588)
at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:205)
at
org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:205)
at
org.biojava.bio.seq.db.biosql.OntologySQL.persistTriple(OntologySQL.java:616)
at org.biojava.bio.seq.db.biosql.OntologySQL.processTerm(OntologySQL.java:262)
at org.biojava.bio.seq.db.biosql.OntologySQL.processTerm(OntologySQL.java:251)
at org.biojava.bio.seq.db.biosql.OntologySQL.addCore(OntologySQL.java:218)
at org.biojava.bio.seq.db.biosql.OntologySQL.<init>(OntologySQL.java:396)
at
org.biojava.bio.seq.db.biosql.OntologySQL.getOntologySQL(OntologySQL.java:71)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.initDb(BioSQLSequenceDB.java:236)
... 2 more
--------------------------------------------------------------------------------
which added a row with '__core_ontology' in the table 'ontology';
When I try to fetch the entry for a second time, I get:
------------------------------------------------------------------------------------------
Exception in thread "main" org.biojava.bio.BioError: Invalid term id 4
at org.biojava.bio.seq.db.biosql.OntologySQL.termForID(OntologySQL.java:691)
at
org.biojava.bio.seq.db.biosql.BioSQLSequenceDB.getOntologyTerm(BioSQLSequenceDB.java:951)
at
org.biojava.bio.seq.db.biosql.FeaturesSQL.retrieveFeatures(FeaturesSQL.java:155)
at
org.biojava.bio.seq.db.biosql.BioSQLAllFeatures.getFeatures(BioSQLAllFeatures.java:145)
at
org.biojava.bio.seq.db.biosql.BioSQLAllFeatures.features(BioSQLAllFeatures.java:73)
at
org.biojava.bio.seq.db.biosql.BioSQLSequence.features(BioSQLSequence.java:237)
at ca.warnex.sab.util.helpers.biosqlTest.main(biosqlTest.java:62)
------------------------------------------------------------------------------------------
The fourth Ontology row is the one with '__core_ontology' in its name.
Any Ideas???
Are you sure the biosql-db schema (biosqldb-mysql.sql v. 1.38) is the wright one to
use ?
Alexandre D.L.
-----Original Message-----
From: Simon Foote [mailto:[EMAIL PROTECTED]
Sent: Tue 6/1/2004 9:05 AM
To: Alexandre Dionne Laporte
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Biojava uses which BioSQL shema version ?
Hi Alexandre,
That version of biosql schema should work fine with the biojava snapshot
you have.
To load a Genbank file into the database, the following code should do
the trick with the various variables set and error handling code added:
BioSQLSequenceDB bsd = new BioSQLSequenceDB(driver, url, user, password,
biodatabase, create);
BufferedReader br = new BufferedReader(new FileReader(inFile));
SequenceIterator si = SeqIOTools.readGenbank(br);
Sequence seq = (Sequence) si.nextSequence();
bsd.addBioEntry(seq);
To write it in Genbank format you can use the getSequence() and
appropriate writeSequence() method for the format you want.
Cheers,
Simon
Alexandre Dionne Laporte wrote:
>Hi,
>
>First of all, here are the softwares I use:
>
>1) Biojava snapshot 'biojava-20040528'
>2) latest biosql shema : biosqldb-mysql.sql v. 1.38
>3) Some of Bioperl 1.4 and bioperl-db projects
>
>
>I would like to store entries from a Genbank file from the NCBI to the
>BioSQL schema using biojava. That I can do with the 'load_seqdatabase.pl'
>script found in bioperl-db without any problem.
>
>In a same way, I would like to retreive sequences with the Biojava package
>and dump it in Genbank file format, as I can do with 'bioentry2flat.pl'
>script.
>
>My question is : Which version of biosqldb should I use with the biojava
>snapshot ?
>
>Thanks,
>
>Alexandre D.L.
>
>_______________________________________________
>Biojava-l mailing list - [EMAIL PROTECTED]
>http://biojava.org/mailman/listinfo/biojava-l
>
>
--
Bioinformatics Programmer
Pathogen Genomics
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561 [F] 613-952-9092
[EMAIL PROTECTED]
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