[EMBOSS] can't access databases indexed by dbifasta

[Marc Logghe]

Hi,
Reminds me of a problem I had a while ago. Maybe it is a similar problem. Have a look at: http://www.hgmp.mrc.ac.uk/Emboss/HYPERMAIL/emboss/emboss.200305/0008.html
HTH,
Marc

> -----Original Message-----
> From: Marcus Claesson [mailto:m.claesson at student.ucc.ie]
> Sent: dinsdag 17 februari 2004 16:24
> To: David Martin
> Cc: emboss at embnet.org
> Subject: Re: [EMBOSS] can't access databases indexed by dbifasta
> 
> 
> Hi,
> 
> I have now changed emboss/emboss.defaults to:
> 
> SET $emboss_db_dir /var/data/blast_db
> 
> DB ecoli.nt [
>    type: "N"
>    format: "fasta"
>    method: "emblcd"
>    dir: "$emboss_db_dir"
>    indexdir: "$emboss_db_dir"
>    file: "ecoli.nt"
> ]
> 
> And get the same negative result:
> 
> [marcus]$ showdb
> Displays information on the currently available databases
> # Name        Type ID  Qry All Comment
> # ====        ==== ==  === === =======
> ecoli.nt      N    OK  OK  OK  -
> 
> [marcus]$ seqret ecoli.nt
> Reads and writes (returns) sequences
> Error: failed to open filename 'ecoli.nt'
> Error: Unable to read sequence 'ecoli.nt'
> Died: seqret terminated: Bad value for '-sequence' and no prompt
> 
> I find this very strange! If you don't know what's wrong 
> would you know
> anywhere else I can get help with this?
> 
> Thanks again.
> 
> Marcus
> 
> 
> On Tue, 2004-02-17 at 15:07, David Martin wrote:
> > On 17/2/04 2:49 pm, "Marcus Claesson" 
> <m.claesson at student.ucc.ie> wrote:
> > 
> > > Thanks for your answer Jerome! But it didn't seem to help 
> me. I added
> > > the indexdir line with the same path (where the index 
> files and fasta
> > > file is) as "dir:". I tried this both with and without setting a
> > > emboss_db_dir variable, but it still didn't work. In 
> other words I can
> > > still only access the database (that shows up in showdb) 
> if I am in that
> > > fasta file directory.
> > 
> > This is because you have not set the file: option? try that 
> and see if it
> > works.
> > in the original example you give the database the same name 
> as the fasta
> > file so it works if it is in the right directory.
> > 
> > > 
> > > Do I need to set this path somewhere else than in 
> emboss.default you
> > > think?
> > 
> > >> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
> > >> 
> > >> 
> > >> DB rbcl [
> > >>     type: N
> > >>     method: emblcd
> > >>     format: fasta
> > >>     dir: $jerome_database_dir/banque1
> > >>     indexdir: $jerome_database_dir/banque1
> >        file: seqfile.fasta
> >        comment: "It is useful to put a description here"
> > >> ]
> > 
> > 
> > ..d
> 
>