[EMBOSS] Problem with showdb and seqret
Guy Bottu
gbottu at vub.ac.be
Tue Feb 24 09:26:27 UTC 2009
Mohd Afiq Hazlami wrote:
> But when
> it comes to 'showdb' tutorial, the program returns this:
Alas, the manual and tutorial are out-of-date. This is an unfortunate chronic
disease of EMBOSS, even if for the rest EMBOSS is great.
Before you can access 'public' sequences using the
<database name>:<sequence identifier>
syntax you must first define databases in the file
<EMBOSS installation dir>/share/EMBOSS/emboss.default
There is a file emboss.default.template with examples.
To get a quick try using the EMBOSS tutorial data you could put the following in
emboss.default :
DB test_embl [ type: N comment: 'testset for EMBL' format: embl
method: emblcd dir: /opt/sw/EMBOSS6/EMBOSS-6.0.1/test/embl
]
Do replace /opt/sw/EMBOSS6/EMBOSS-6.0.1/test/embl by
<EMBOSS download dir>/test/embl
You will note that this directory does contain sequences and indexes.
You can then do
showdb
entret test_embl:Z11115
You can read more about it at
http://emboss.sourceforge.net/docs/themes/Databases.html
A question for the EMBOSS development team : what is the status of the new
EMBOSS manual ?
Regards,
Guy Bottu,
Belgian EMBnet Node
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