[Bioperl-l] Sending Accession Numbers to Blast Server

Agrin, Nathan Nathan.Agrin@umassmed.edu
Fri, 13 Dec 2002 11:15:26 -0500

I'm trying to get a script running using bioperl such that I can send a list of accession numbers to blast servers and retrieve the matches.  My problem is that anytime I use something like this:

for ($i=0; $i<$#anum+1; $i++) {
my $db = new Bio::DB::SwissProt;
my $seq = $db->get_Seq_by_version('$anum[$i]');

I get an error that says 'Implementing class should define this method'
and if I just try to bypass defining the accession number and pass the straight accession number to submit_blast('$anum[$i]') I get an error telling me it's not a valid blast input.  I'm trying to run a blastx search which seems to work fine over the web when I input the accession numbers.

Any ideas would be appreciated.