List of queries with getz

Peter Rice pmr at sanger.ac.uk
Tue Nov 24 08:52:02 EST 1998


Heikki Lehvaslaiho <heikki at ebi.ac.uk> writes:

> Olivier POIROT wrote:
> > Is it possible to use a file containing a list of Ids with getz (SRS
> > version 5.1)?
> Dear Olivier,
> I suppose you mean lists like these:
> %  more  my.list
> EMBL:AB015259
> EMBL:AB015260
> EMBL:AB015261
> EMBL:AB015262
> %
> getz needs its input formatted in a slightly different way. Let's
> write a script, in icarus of course, that does what you want and can
> be extended as needed. 

Not really what is needed. That Icarus script just runs getz for each
sequence and writes the results to stdout.

I have asked Thure several times for the SRS 4 capability to use a list
of entries as a query. Then you can do things like:

getz '@my.list > swissprot'
getz '@my.list' -f 'id acc des'
getz '@my.list ! (embl < emblnew)'

So far no sign of this appearing, though Thure promised it was not
difficult.  I really miss this capability. The lists can be created by
getz (they are the default output) but cannot be used since SRS 4 went
away.

-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/




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