[EMBOSS] can't access databases indexed by dbifasta

[Marcus Claesson]

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