List of queries with getz

Marco Pagni Marco.Pagni at igbm.unil.ch
Tue Dec 8 03:14:14 EST 1998


Peter Rice wrote:

> 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/

I have exactely the same need, and I am sure that we are more than two SRS
users with the same need. The rationale for this is that  SRS  outputs
reflect the
databases content which are not free from erroneous annotations. To be
fully biologically
significant,  a few entries must often be added to or removed from result
sets. And
unfortunately such "manually" corrected cannot be read by SRS as input for
further
querying databases.

Regards,

Marco Pagni
Swiss Institute of Bioinformatics
mpagni at igbm.unil.ch





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