[EMBOSS] can't access databases indexed by dbifasta

[Jérôme Laroche]

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
>
>