other indices

[Peter Rice]

Joerg Schaber wrote:

> dbiflat allows to index other fields except id and accession number like 
> sequence version (seqv), description (des), keywords and taxon. However, 
> in the example databases that come with EMBOSS I found only field 
> definitions like 'fields: "sv des org key"'. So do I access the 
> additional indices (e.g. in seqret) via 'seqret-sv:\*', 
> 'seqret-des:\*','seqret-org:\*','seqret-key:\*', respectively? 
> 'seqret-taxon:\*', 'seqret-seqv:\*', and 'seqret-keyword:\*'  did not work.

For a database called schaber

dbiflat -fields "acnum,seqvn,des,keyword,taxon"

In the emboss.default definition:

DB schaber  [ type: P format: swiss method: emblcd
   dir: /data/schaber
   indexdir: /data/schaber
   comment: "Flatfiles database, all fields indexed"
   fields: "sv des org key"
]

In EMBOSS programs, use the USA:

'schaber-sv:\*'
'schaber-des:\*'
'schaber-org:\*'
'schaber-key:\*'

The confusion comes because the database definition (and the USA syntax) 
uses the field names in common use (e.g. in SRS) and dbiflat uses the 
EMBLCD/Staden index file names that dbiflat will be writing.

regards,

Peter

-- 
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Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723