[EMBOSS] can't access databases indexed by dbifasta

[Marcus Claesson]

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.

Do I need to set this path somewhere else than in emboss.default you
think?

Marcus



On Tue, 2004-02-17 at 13:57, Jérôme Laroche wrote:
> Hi Marcus,
> 
>   it seems that your file .emboss_default don't have the line to specify 
> the location of the indexed database (check the last line of my 
> example).
> Also, you can add this line at the begining of your file (setting a 
> variable for the path of your database) so if you move your database 
> and your index, you just have to modify the path at this line.
> 
> 
> 
> SET jerome_database_dir /cbi/people/jlaroche/data/banquesemboss
> 
> 
> DB rbcl [
>     type: N
>     method: emblcd
>     format: fasta
>     dir: $jerome_database_dir/banque1
>     indexdir: $jerome_database_dir/banque1
> ]
> 
> 
> 
> Jerome
> 
> Centre de bioinformatique
> Pavillon Charles-Eugène-Marchand
> Bureau 4233d
> tél: 418-656-2131 poste 6184
> fax: 418-656-7176
> www.bioinfo.ulaval.ca
> 
> 
> Le 04-02-17, à 05:58, Marcus Claesson a écrit :
> 
> > Hello,
> >
> > I have a silly little problem indexing databases in Emboss-2.8.0. After
> > running dbifasta and adding DB entries in emboss.default I can only
> > access the database when being in the same directory as the fasta file.
> > Here is what I did:
> >
> > [blast_db]$ uname -a
> > Linux neo.ucc.ie 2.4.9-e.35enterprise #1 SMP Tue Dec 23 00:06:16 EST
> > 2003 i686 unknown
> >
> > [blast_db]$ pwd
> > /var/data/blast_db
> >
> > [blast_db]$ ll ecoli.nt
> > -rw-r--r--    1 marcus   bioinfo   4763013 Jan 15 01:38 ecoli.nt
> >
> > [blast_db]$ dbifasta
> > Index a fasta database
> >     simple : >ID
> >      idacc : >ID ACC
> >      gcgid : >db:ID
> >   gcgidacc : >db:ID ACC
> >       dbid : >db ID
> >       ncbi : | formats
> > ID line format [idacc]:
> > Database directory [.]: /var/data/blast_db
> > Wildcard database filename [*.dat]: ecoli.nt
> > Database name: ecoli.nt
> > Release number [0.0]:
> > Index date [00/00/00]:
> >
> > [blast_db]$ ll entrynam.idx division.lkp acnum.*
> > -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.hit
> > -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 acnum.trg
> > -rw-rw-r--    1 marcus   bioinfo       330 Feb 17 10:39 division.lkp
> > -rw-rw-r--    1 marcus   bioinfo       300 Feb 17 10:39 entrynam.idx
> >
> > Added these lines in /usr/local/EMBOSS-2.8.0/emboss/emboss.default:
> >
> > DB ecoli.nt [
> >    type: "N"
> >    format: "fasta"
> >    method: "emblcd"
> >    dir: "/var/data/blast_db/"
> > ]
> >
> > [blast_db]$ showdb
> > Displays information on the currently available databases
> > # Name        Type ID  Qry All Comment
> > # ====        ==== ==  === === =======
> > ecoli.nt      N    OK  OK  OK  -
> >
> > [blast_db]$ cd ~
> >
> > [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
> >
> > But it works when I'm the same directory as ecoli.nt:
> >
> > [blast_db]$  seqret ecoli.nt
> > Reads and writes (returns) sequences
> > Output sequence [ae000111.fasta]:
> > etc...
> >
> > Clearly it must be possible to access ecoli.nt from other directories?
> >
> >
> > Extremly grateful for any help on this!
> >
> > Regards,
> > Marcus
> >
> >
>