getz problem

Tim Cutts timc at chiark.greenend.org.uk
Wed Aug 29 03:11:50 EST 2001


In article <3B864A35.908A3F5F at well.ox.ac.uk>,
John Broxholme  <johnb at well.ox.ac.uk> wrote:
>
>Any ideas why the following should not work:
>
>johnb at zeon /// getz "libs=[embl-Description: abc2*] & [libs-org:human]"
>error: unknown set or databank, "libs"
>
>when the following does:
>
>johnb at zeon /// getz "[embl-Description: abc2*] & [embl-org:human]"
>EMBL:AF216833
>EMBL:HS18235

libs is for combining complete databases, whereas you're trying to treat
it as a result set.

In this case you don't need it.  The second version of your query is
the correct form, but you could use the following more verbose form,
which is probably what you were aiming at:

getz "[libs={embl}-des: abc2*] & [libs-org:human]"

although I just tried a similar query here, using SRS 5.1, and it was
very slow indeed, so there seems to be a potentially really bad
implementation inefficiency in SRS 5.1 for this sort of query.
Hopefully it's better in SRS 6.x

I use both result sets and libs={} assignments to always retrieve the
latest version of a sequence from genbank and genbanknew:

For example:

getz -e "(q22714=[libs={genbank genbanknew}-id:X12345]) ! q22714<genbanknew"

This query works as follows:

1)  Query both Genbank and GenbankNew for id X12345, and store the
results in set q22714
2)  Find those entries in q22714 which have a link to genbanknew (in
other words, have an updated version in genbanknew)
3)  Remove these entries from the result set.

Hopefully this neatly demonstrates the difference between querying
multiple libraries and assigning to a result set.

Tim.

-- 
"It is the job of Sales and Marketing to insulate those who know what
they're talking about from each other"
  -- I know who said this, but I'm not telling.





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