[EMBOSS] case sensitive identifiers
pmr at ebi.ac.uk
Fri Sep 29 10:27:51 UTC 2006
Guy Bottu wrote:
> For the moment our emboss.default contains :
> DB pdbprot [ type: P format: fasta comment: 'protein sequences from PDB'
> methodquery: app app: "/nfsben/srs/bin/linux73/getz -e '[pdbprot-id:%s]'"
> methodall: direct dir: /nfsben/srs/data/blast/dbfb/pdb file: pdb
That raises a new problem .... the "app" method will work, but "srs" and
"srswww" will not.
They search for a pdbprot-acc match and there is no acc field.
I will add a new database attribute hasaccession (default "Y") so
searches know whether the acc field can be used. Unfortunately the
fields attribute is defined as "everything except id and acc" so I
cannot use it.
So, there will be 2 new (and for the first time boolean) attributes for
databases. To use them, you will need:
These will also be the first to use the default values for database
attributes! All other default values are empty strings :-)
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