dbiflat question

[Marc Logghe]

Thanks for the reply !
That is what I have figured out:
when you run
dbiflat -idformat genbank -directory /data/genbank -filenames gbest226.seq
in the index directory (e.g. /data/emboss/est) has the same effect as
running 
dbiflat -idformat genbank -directory /data/genbank -indexdirectory
/data/emboss/est -filenames gbest226.seq
meaning, the index files are created in the desired place. But still the
sequences themselves are not accessible using the mentioned entry in
emboss.default ('seqret est -firstonly' gives a segmentation fault). I
suppose the 'directory' key should point to the indexdirectory, right ?
Because, the index itself should be pointing to the correct sequence path.
At least that is what I expect.
And indeed, as suggested by Tony, everything worked fine when putting index
and sequence files in the same directory (indexdirectory and directory are
the same).
OK, just tried something which appears to work now. Switch to the first
scenario again: separate paths for index and sequence files. When I changed
the emboss.default to the following, everything worked fine:

DB est [
   type: N
   format: genbank
   method: emblcd
   indexdirectory: /data/emboss/est
   directory: /data/genbank
]

Apparently you have to set the indexdirectory and directory explicitely in
the configuration file also; pointing to the indexdirectory alone is not
sufficient !
Regards,
Marc
 
> -----Original Message-----
> From: Tony Pemberton [mailto:pemberaj at pugh.bip.bham.ac.uk]
> Sent: Wednesday, May 07, 2003 1:18 PM
> To: Marc Logghe
> Cc: Emboss (E-mail)
> Subject: Re: dbiflat question
> 
> 
> On Wed, 7 May 2003, Marc Logghe wrote:
> 
> > Hi all,
> > I feel a little dumb but I'll ask it anyhow. I seem not to 
> succeed in
> > creating indices for a database using dbiflat.
> > As a test I just wanted to index the genbank file 
> /data/genbank/gbest226.seq
> > Ok, I wanted my indices to be in /data/emboss/est
> > so I have run dbiflat in that folder.
> > dbiflat -idformat genbank -directory /data/genbank 
> -filenames gbest226.seq
> > -dbname est
> > I added this entry to emboss.default
> > DB est [
> >    type: N
> >    format: genbank
> >    method: emblcd
> >    directory: /data/emboss/est
> > ]
> >
> > But, you guessed it, this did not work.
> > What am I doing wrong here ? What happens with the passed 
> dbname (could not
> > find any file with that name after running dbiflat) ?
> > TIA,
> > marc
> >
> > ***********************************************************
> > Marc Logghe, Ph.D.
> > Senior Scientist
> > Scientific Computing Group
> > deVGen
> > Technologiepark 9
> > 9052 Zwijnaarde
> > Belgium
> > tel: +32 (0) 9 324 24 83
> > fax: +32 (0) 9 324 24 25
> > ***********************************************************
> >
> >
> >
> 
> Marc,
> 
> You need the .seq file also to be in the directory where you run
> dbiflat. Or make symbolic links!
> 
> You will note that the dialogue of dbiflat asks about the files to
> process (*.seq). At this stage, I think I am correct in saying, that
> the database directory file emboss.default is not operable. This
> merely directs the user programs e.g. seqret to the formatted
> database (indeces) as shown by showdb.
> 
> Regards,
> 
> Tony
> 
> 
> *********************************************************************
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> c/o Dept. Rheumatology,        Fax:  +121-414-6794
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