[EMBOSS] Database access external app

[Marc Logghe]

Hi Stefanie,
Can you show the actual entry in your emboss.default file, or eventual error messages when running the emboss command ?
We use exactly the same system for the worm chromosomal sequences for instance. Every chromosome is a separate blastable 'database'. worm_chromosomes.nal makes them look like 1 big.
The entry looks like this:
DB worm_chromosomes [
   type: N
   format: ncbi
   method: app
   app: "fastacmd -d worm_chromosomes -s %s"
]

HTH,
Marc

> -----Original Message-----
> From: Stefanie Lager [mailto:stefanielager at fastmail.ca]
> Sent: vrijdag 13 februari 2004 8:55
> To: emboss at embnet.org
> Subject: [EMBOSS] Database access external app
> 
> 
> Hi,
> 
> I'm trying to retrieve entries in EMBOSS using fastacmd as an external
> application. It works nice as long as the database, indexed with
> formatdb, is a singe fasta file. But when I have big 
> databases that are
> split up in volumes and use a .nal file with the names of the 
> idividual
> files it doesn't work with EMBOSS anymore. Does anyone have experience
> with fastacmd and EMBOSS database indexing in combination 
> with databases
> split into volumes?
> 
> Stefanie 
> _________________________________________________________________
>     http://fastmail.ca/ - Fast Secure Web Email for Canadians
>