[EMBOSS] case sensitive identifiers

Peter Rice 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:

caseidmatch: "Y"
hasaccession: "N"

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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