dbiflat question

[Tony Pemberton]

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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