[EMBOSS] Antwort: "entret", "seqret", & "whichdb" don't work

David.Bauer at SCHERING.DE David.Bauer at SCHERING.DE
Wed Jul 12 05:47:34 UTC 2006


the emboss.default file, which comes with the distribution, contains some
example definitions for databases.
But they don't work out of the box.
In principle there are two ways for database access from emboss:
You can either have the data on a local file system and index them with
the emboss utilities (dbxflat, dbxfasta etc.) or you can configure emboss
to access remote databases via http.
There is a chapter about database configuration in the documentation
which explains in detail how to configure database access.

Hope this helps,

emboss-bounces at lists.open-bio.org schrieb am 11/07/2006 19:16:06:

> Dear Sir,
> The commands "entret", "seqret", and "whichdb" don't work on my intel
> Mac.
> http://www.csc.fi/molbio/progs/emboss/doc/programs/html/entret.html
> $entret tembl:hsfau
> Reads and writes (returns) flatfile entries
> Error: failed to open filename 'tembl'
> Error: Unable to read sequence 'tembl:hsfau'
> Died: entret terminated: Bad value for '-sequence' and no prompt
> http://www.csc.fi/molbio/progs/emboss/doc/programs/html/seqret.html
> $seqret
> Reads and writes (returns) sequences
> Input sequence(s): tembl:hsfau
> Error: failed to open filename 'tembl'
> Error: Unable to read sequence 'tembl:hsfau'
> http://www.csc.fi/molbio/progs/emboss/doc/programs/html/whichdb.html
> $whichdb -showall
> Search all databases for an entry
> ID or Accession number: hsfau1
> Output file [outfile.whichdb]: stdout
> <Nothing were shown>
> [About my Mac]
> Mac OS X 10.4.6
> Darwin 8.6.1
> MacBookPro1,1
> Intel Core Duo
> I am looking forward to hearing from you.
> Sincerely yours,
> Haruo Suzuki
> --------------------------------------
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