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

[charles-listes-emboss at plessy.org]

Le Wed, May 30, 2007 at 02:33:11PM +0100, Peter Rice a écrit :
> 
> Aha ... mirbase is in EMBL format .. except the IDs are in lower case. All other 
> EMBL/UniProt databases are in upper case.

Dear Peter,

I tried to index RepBase today, and I ran into another problem: not only
the IDs are lower case, but also it does not provide accession numbers.
I used the following for indexing:

dbxflat -dbname repbase\
	-dbresource embl\
	-idformat EMBL\
	-filenames '*ref'\
	-directory .\
	-fields id,org,key,des\
	-release 12.04

DB repbase [
  type: N
  format: embl
  method: emboss
  directory: /home/charles/databases/RepBase12.04.embl
  file: *.ref
  fields: "id key des org"
  comment: "Repeats"
]

However, seqret still complains that the AC field is not indexed:

gslc12『RepBase12.04.embl』$ seqret repbase:RLTR19_MM
Reads and writes (returns) sequences

   EMBOSS An error in ajindex.c at line 3027:
Cannot open param file /home/charles/databases/RepBase12.04.embl/repbase.pxac


I will rebuild emboss with the patched version of dbiflat and see if it
can work instead.


Have a nice day,

-- 
Charles