[EMBOSS] Antwort: Genbank GI fetching?

[david.bauer at bayerhealthcare.com]

Hi Niels,

when indexing the sv field, dbxflat indexes the words as they are there.
This means that 'GI:' becomes part of the indexed word.
So

seqret test:GI:106880293
or
seqret test:\*106880293

will return the requested entry.
And you also need the line

fields: "id acc sv des key org" 

in your database definition.

HTH,
David.

Niels Larsen <niels at genomics.dk> schrieb am 14/06/2007 11:53:34:

> Hi .. I did run dbxflat like this
> 
> dbxflat -dbname test -dbresource test -idformat gb -filenames \
> 'gbbct7.seq' -directory . -fields=id,acc,sv,des,key,org
> 
> and got an index where entries can be fetched with
> 
> seqret test:AM260486 -stdout -auto
> 
> but not with
> 
> seqret test:106880293 -stdout -auto
> 
> where 106880293 is the GI number from the AM260486. Maybe
> I am specifying the usa wrong .. ?
> 
> Niels L
> 
> david.bauer at bayerhealthcare.com wrote:
> > Hi,
> > 
> > as default it indexes only ID and ACC. If you want GI indexed, you 
must 
> > use the -fields option and specify also sv (sequence version) to be 
> > indexed.
> > 
> > David.