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

Magic Fang fangl at genomics.org.cn
Thu Sep 11 02:43:26 EDT 2003


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.




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