[EMBOSS] external and app

[Marc Logghe]

Hi,
Just wondering, what happens if you use entret in stead of seqret.
EMBOSS is supposed to just return the 'sequence' (in this case pfam
result), unaltered, unparsed. When you use seqret, EMBOSS will parse the
output and try to make a sequence out of it.
HTH,
Marc


> -----Original Message-----
> From: owner-emboss at hgmp.mrc.ac.uk 
> [mailto:owner-emboss at hgmp.mrc.ac.uk] On Behalf Of Guy Bottu
> Sent: Friday, June 03, 2005 12:03 PM
> To: Alexis Torrano Martinez; emboss at embnet.org
> Subject: Re: [EMBOSS] external and app
> 
> On Fri, Jun 03, 2005 at 11:15:10AM +0200, Alexis Torrano 
> Martinez wrote:
> > 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"
> >  	]
> 
> 	Dear Alexis,
> 
> Your problem is as good as certain that the program defined as "app" 
> should return a sequence to standard output, so that EMBOSS 
> can take it. 
> And this is not what hmmsearch does. Furthermore, hmmsearch 
> searches a HMM against a databank of sequences ; you seem to 
> want to search a sequence against a databank of HMM's 
> (Pfam_ls), for which you need hmmpfam. It is maybe a good 
> idea to install the Embassadir HMMER. Note however that 
> ehmmpfam needs the user to specify where the databank is. At 
> the BEN site I have a little bit "hacked" the program so that 
> it uses Pfam_ls by default (and still lets the user choose an 
> alternative). If you are interested I can send you a mail 
> with "how to".
> 
> 	Guy Bottu,
> 	Belgian EMBnet Node
> 
>