[EMBOSS] external and app
Alexis Torrano Martinez
atorrano at lsi.upc.edu
Fri Jun 3 09:15:10 UTC 2005
Hello
I am trying to execute hmmsearch from EMBOSS. This way I want to have
a kind of wrap over the DDBB and retrieval apps.
DB Pfam [
method: "app"
comment: "Pfam with HMMER indexing"
app: "$HMMERBIN/hmmsearch $EMBOSS_DATA/pfam/Pfam_ls %s"
]
That is my DB specification for EMBOSS. How should I run seqret
to execute properly hmmsearch?
seqret Pfam:$HOME/soft/hmmer/last/tutorial/7LES_DROME
And the next error was unexpected :
Error: Unable to read sequence
'Pfam:/usr/usuaris/it/inb/soft/hmmer/last/tutorial/7LES_DROME'
As tutorial says, if you specify external, %s receives as value the
second field of the query (ID from seqret DB:ID).
There is a way to call hmmsearch from EMBOSS?
A lot of thanks.
Regards.
Alexis Torrano.
--
-----------------------------------------------------
Alexis Torrano Martinez
Instituto Nacional de Bioinformatica (INB) Nodo
Computacional GNHC-2
UPC-CIRI
c/. Jordi Girona 1-3
Modul C6-E201 Tel. : 934 011 650
E-08034 Barcelona Fax : 934 017 014
Catalunya (Spain) e-mail : atorrano at lsi.upc.edu
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