DataLib management

Aengus Stewart aengus.stewart at
Thu Mar 20 17:27:31 UTC 2003


Sorry in advance folks, but I am making a concerted effort to set up the
datalibs for access by EMBOSS and as a result it has prompted a few

First of all a comment - I have had a look at the documentation for both
dbiflat and dbigcg, and neither makes any note of the fact that both
ACNUM and ID fields are indexed by default.  In fact ID is not really
mentioned at all so when you look at the documentation for the '-fields'
flag it appears that there are only 5 possible fields to index.

A small point, there is an inconsistency between the allowed values for
-fields and the values for the fields: tag in emboss.default

-fields flag can use any of - acnum,seqvn,des,keyword,taxon

fields: tag can use any of - acc id sv des org key

I know they dont have to be the same, it just seemed odd.

showdb -fields


Died: unknown qualifier -fields

Also dbigcg/dbiflat asks for the release number and date.  I would like
showdb to pick this information up but the only way I can see of doing
this is a search/replace on 'release:X.Y' in emboss.default

What does dbigcg/dbiflat do with the release/date info?

Sorry again for all the queries.


Aengus Stewart                               
aengus.stewart at
Computational Genome Analysis Laboratory      Tel: +44 (0)20 7269 3679
Cancer Research UK
Lincoln's Inn Fields, Holborn, London, WC2A 3PX, UK

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