SRS5 Bug in embl

John Peden johnp at molbiol.ox.ac.uk
Fri Jun 6 14:02:38 EST 1997


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]+|

Via the web
select new srs session
select embl and emblnew
use these ID's as your query     SMU75476|SMD031
check all three sequences
select save button
select save complete entry 
select save


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




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