[EMBOSS] Indexing the ID field of EMBL-formatted databases.

[Charles Plessy]

Dear list,

I have tried to index mirbase, the miRNA database, with dbiflat, but in that
case I can only retrieve the seqences by their accession numbers, and not by
their IDs:

gslc12『mirbase3』$ seqret mirbase:MI0004658 stdout
Reads and writes (returns) sequences
>mmu-mir-690 MI0004658 Mus musculus miR-690 stem-loop
uguguuuuuguggagcuaauuggcuguauuaaagugcuaguaagaaacauucuccuccag
cuggagagauggcucagcuguuaaaggcuaggcucacaaccaaaauaua

gslc12『mirbase3』$ seqret mirbase:mmu-mir-690 stdout
Reads and writes (returns) sequences
Error: Unable to read sequence 'mirbase:mmu-mir-690'
Died: seqret terminated: Bad value for '-sequence' and no prompt

gslc12『mirbase3』$ seqret mirbase-ID:mmu-mir-690 stdout
Reads and writes (returns) sequences
Error: Unable to read sequence 'mirbase-ID:mmu-mir-690'
Died: seqret terminated: Bad value for '-sequence' and no prompt

gslc12『mirbase3』$ seqret mirbase-id:mmu-mir-690 stdout
Reads and writes (returns) sequences
Error: Unable to read sequence 'mirbase-id:mmu-mir-690'
Died: seqret terminated: Bad value for '-sequence' and no prompt

Here is the command line I used:

 dbiflat -dbname mirbase\
                 -idformat EMBL\
                -directory .\
                -filenames miRNA.dat\
                -release 9.1\
                -date `date +%d/%m/%y`\
                -outfile /dev/stdout

And here is the embossrc I use:

DB mirbase [
  type: N
  format: embl
  method: emblcd
  directory: /usr/share/mirbase/emboss
  file: *.dat
]

Is it a bug, or did I miss something ?

Have a nice day,

-- 
Charles Plessy
http://charles.plessy.org
Wako, Saitama, Japan