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
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