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Link problem for getz (srs5.05)

Peter Rice pmr at sanger.ac.uk
Fri Oct 24 04:02:05 EST 1997


joew at base4.com (Joe Wang) writes:

> 
> According to the SRS menu, if I want to get all human
> CDSs from GenBank, I should do:
> getz '[genbank-org:homo] \> [genbank-ftk:cds]' -f seq
> 
> Instead of the CDSs, I get the entire sequence tries.
> 
> When I do:
> getz '[genbank-ftk:cds] \< [genbank-org:homo] ' -f seq
> 
> I get all the CDSs from GenBank (not only the human ones).
> 
> If I don't use the escape "\", I get nothing.
> 
> It looks like that the linking function ">" or "<" is not working.
> 
> Any suggestions?

The "\>" is wrong - you should just use ">" or "<".

I suspect your GenBank release does no have "Homo" explicitly in the taxonomy.
Maybe the human entries are indexed only as "homo sapiens". If so, the
[genbank-org:homo] part of the query will not work.

You can quickly check this with:

(srs5) getz -lv  '[genbank-org:homo*]'
(srs4) getz -rep '[genbank-org:homo*]'

Yikes - just tried that here with EMBL 51, and found a really weird one:

% getz -lv  '[embl-org:homo*]'

////////////////////////////////////////////////////////////////////////////

Values in "EMBL"
    homo                                                              829492
    homo sapiens                                                      829491

////////////////////////////////////////////////////////////////////////////

report of query "[embl-org:homo*]"

.. and the reason is, two sets of OS and OC lines:

% getz "[embl-org:homo\!homo sapiens]" -e|more
ID   H17BHYD    standard; DNA; HUM; 21764 BP.
XX
AC   M84472;
XX
NI   g806392
XX
DT   25-DEC-1992 (Rel. 34, Created)
DT   13-OCT-1996 (Rel. 49, Last updated, Version 11)
XX
DE   Human 17-beta-hydroxysteroid dehydrogenase (EDH17B1 and EDH17B2)
DE   genes, complete coding regions and flanks.
XX
KW   17-beta-dehydrogenase; 17-beta-hydroxysteroid dehydrogenase;
KW   Alu repeat; estradiol.
XX
OS   Homo
OC   Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata;
OC   Vertebrata; Eutheria; Primates; Catarrhini; Hominidae.
XX
OS   Homo sapiens (human)
OC   Eukaryotae; mitochondrial eukaryotes; Metazoa; Chordata;
OC   Vertebrata; Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX






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