SRS5 Bug in embl

Martin Hilbers mph at dl.ac.uk
Mon Jun 9 03:43:22 EST 1997


John Peden wrote:
> 
> Hi All
> 
> 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"
> 
> worf.molbiol.ox.ac.uk   gcg embl format
>  says syntax error production `seq' :
>   |àØÿÿÿÿÿÿ>>>>SMD031  5/97  2BIT  Len: 2195|
>   .....................................^
>     no match with |^[0-9]+|
> 
> www.ebi.ac.uk           gcg embl format
>  says syntax error
>   production `seq' :
>    | 2195|
>    .....................................^
>    no match with |^[0-9]+|
> 
> 
> From the command line:
> 
>  getz -e '[libs={embl emblnew}-id:SMU75476|SMD031]'
> 
> Generates an error .... But
> 
> getz -e '[libs={     emblnew}-id:SMU75476|SMD031]'
> getz -e '[libs={embl        }-id:SMU75476|SMD031]'
> 
> work fine ...
> 
> john

Well.. on our site (http://www.seqnet.dl.ac.uk/srs5) I don't
get an error, but srs does refuse to retrieve an entry with
the same number from both embl and emnew (called eupdates
at our site)

Martin

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