[EMBOSS] Antwort: Genbank GI fetching?
david.bauer at bayerhealthcare.com
david.bauer at bayerhealthcare.com
Thu Jun 14 11:17:20 UTC 2007
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.
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