[Bioperl-l] Bio::DB::GenBank problem

[Lincoln Stein]

Just forget about requesting the format.  It works fine with both AC130605 and 
AC130605.2 with a simple:

	$gb = Bio::DB::GenBank->new();
	$seq=$gb->get_Seq_by_acc('AC130605');

The -format argument is undocumented and intended solely for internal use, 
which means that if you use it, expect to get burned.

Lincoln



On Thursday 11 September 2003 02:43 am, Magic Fang wrote:
> Dear my colleagues, can anybody tell me why the codes below get different
> result: use Bio::DB::Query::GenBank;
> use Bio::DB::GenBank;
>
> $gb=Bio::DB::GenBank->new(-format => 'fasta');
> $gb->proxy([ftp, http], 'http://192.168.4.7:80');
> $seq=$gb->get_Seq_by_acc('AC130605.2');
> print $seq->display_id, "\t", $seq->length, "\n";
>
> get normal result
>
> ----------------------------------------------------------------
> use Bio::DB::Query::GenBank;
> use Bio::DB::GenBank;
>
> $gb=Bio::DB::GenBank->new(-format => 'fasta');
> $gb->proxy([ftp, http], 'http://192.168.4.7:80');
> $seq=$gb->get_Seq_by_acc('AC130605');
> print $seq->display_id, "\t", $seq->length, "\n";
>
> ------------- EXCEPTION  -------------
> MSG: acc does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:177 STACK toplevel
> db_test.pl:6
>
> -------------------------------------------------------------------
>
> use Bio::DB::Query::GenBank;
> use Bio::DB::GenBank;
>
> $gb=Bio::DB::GenBank->new(-format => 'genbank');
> $gb->proxy([ftp, http], 'http://192.168.4.7:80');
> $seq=$gb->get_Seq_by_acc('AC130605');
> print $seq->display_id, "\t", $seq->length, "\n";
>
> ------------- EXCEPTION  -------------
> MSG: acc does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:177 STACK toplevel
> db_test.pl:6
>
> --------------------------------------
>
> ----------------------------------------------------------------------
> use Bio::DB::Query::GenBank;
> use Bio::DB::GenBank;
>
> $gb=Bio::DB::GenBank->new(-format => 'genbank');
> $gb->proxy([ftp, http], 'http://192.168.4.7:80');
> $seq=$gb->get_Seq_by_acc('AC130605.2');
> print $seq->display_id, "\t", $seq->length, "\n";
>
> ------------- EXCEPTION  -------------
> MSG: acc does not exist
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm:177 STACK toplevel
> db_test.pl:6
>
> --------------------------------------
>
> Thank you.
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)