[EMBOSS] Question regarding seqret

[Peter Rice]

Jean Mao wrote:
> Hi, 
> I have a question hopefully someone can help me about it.
> 
> I downloaded the gbrvt1.seq file from ftp://ftp.ncbi.nih.gov/genbank/ as a test, gunzip and index it with dbxflat (I know it's not > than 2gb):
> 
> %  dbxflat -dbname=testdb -dbresource=embl -idformat=gb -directory=. -fields='id,acc,sv,des' -filenames='gbvrt*.seq' -indexoutdir=. -release=0.0 -date='00/00/00'
> 
> Then I run 'seqret' but failed to retrieve entries using 'sv' or 'des' fields:

I didn't see an answer to this one, but I suspect you have already figured it out.

dbixflat and dbiflat will have created the sv and des indices.

You have to edit the database definition in emboss.default to say the fields exist.

    fields: "sv des"

then seqret and other programs will know they can use them.

Yes, in theory seqret could work out what indices are available for a dbxflat or 
dbiflat indexed database - but it would be more difficult for an SRS or SRSWWW 
database (for example) so we depend on the database definitions.

Hope that helps,

Peter