bug in reading GCG databases

[Karl-Heinz Glatting]

Dear all,

There is probably a bug in reading GCG formatted databases via
EMBOSS when using expressions like swissprot:* (other wildcard
specifications and extracting entries by name or so do work).
The first sequence is read properly but afterwards everything is
out of sync. I wrote a small emboss application which does nothing
more than ajAcdGetSeqall and a loop over ajSeqallNext.
I found the problem also when using applications like fuzzpro
or water.

I fixed this by deleting line 1994

  ajFileGets (qryd->libs, &line);

in routine seqGcgReadSeq in ajseqdb.c and it seems to work now
but because I don't understand what this line was good for :-)
I'am not sure whether it will work in all possible cases.

BTW, is it true that subsections do not work for GCG formatted
databases? When I define a database like Pir1 as an example
and use pir1:* I get the whole PIR database.

best regards,

Karl-Heinz



Karl-Heinz Glatting
Bioinformatics Service Group
Department of Molecular Biophysics
Deutsches Krebsforschungszentrum (DKFZ)
(German Cancer Research Center)
Heidelberg, Germany
E-Mail: glatting at dkfz-heidelberg.de