[EMBOSS] can't access databases indexed by dbifasta

[Marcus Claesson]

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