[Bioperl-l] Each_DBLink : only returning 1 entry ?

[Ewan Birney]

On Thu, 30 Aug 2001, Jean-Jack M. Riethoven wrote:

> 
> > > that tells me this sequence (or acc_number) is in fact part of EMBL
> > > (Genbank/DDBJ), or SWISS_PROT, or...
> >
> > $dblink->database()
> 
> *chuckle*
> 
> I know $dblink->database() but it returns the database name of a
> crossreference (the DR stuff in EMBL flatfiles).
> 
> What I need is the database code of the main seq object:
> 
> $seq->database()
> 
> In my example, X02158 is the accession_number, HSERPG the display_id.
> DBLink only lists some GDB and SWISS-PROT stuff in this example.
> 
> Normally I would obviously know if I get this from EMBL, Genbank, DDBJ, or
> something else. In my script I'd like to circumvent guessing work though -
> I know the main database code is not in the EMBL flatfile itself. Would it
> be possible to have a stub function that returns the input format (from
> Bio:SeqIO) as textstring?

Possible. I don't particularly like this. I think it is the responsibility
of how you got the file. 


ie - you can get a sequence from a fasta *file* from EMBL, Swissprot,
Genbank etc *databases*. The format and the data source are really
orthogonal