SRS5 Bug in embl

Peter Rice pmr at sanger.ac.uk
Mon Jun 9 05:27:28 EST 1997


John Peden <johnp at molbiol.ox.ac.uk> writes:
> There appears to be a bug in the embl databases under srs5. I have
> included an example below ... the problem is present on other sites. It
> also appears to be database format (GCG/Native) independent (though the
> error message varies between formats).
> 
> 
> Example
> Via the web
> select new srs session
> select embl and emblnew
> use these ID's as your query     SMU75476|SMD031
> check the boxes for the three sequences
> select save button
> select save complete entry =
> 
> select save
> 
> 
> Errors Messages are:
> 
> www.sanger.ac.uk        native embl format   =
> 
>  says "not possible to write to token table "sequence"

I can get this with just SMD031 as the query. Seems to have a problem
with retrieving from EMBL and EMNEW.

Running wgetz from the command line simply hangs on the second entry.

The Sanger Centre message "not possible to write to token table
"sequence" is apparently caused by an extra call in embl.is to pick up
the entry name ("$Request:entry") inserted by Thure some time back to
fix a different problem.

On the EBI server, I see no ID for the EMBLNEW entry. The ID is present
on the Sanger Centre server.

For comparison, the Sanger Centre has EMBL and EMBLNEW indexed in the
original flat file version. We made a change to wgetz (with Thure) to
fix an EMBL wgetz bu when displaying fields from multiple entries.
We also have a fix in embl.is to put an entryname in the header in FASTA
format which is needed when the database is in the flatfile version.

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/




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