[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Fri Sep 12 10:19:56 EDT 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv14997

Modified Files:
	LocalServices.pm 
Log Message:
needed in order to run as a CGI, since STDOUT is co-opted during the retrieval somehow

moby-live/Perl/scripts/Services LocalServices.pm,1.32,1.33
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.32
retrieving revision 1.33
diff -u -r1.32 -r1.33
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/08/16 17:29:32	1.32
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/09/12 14:19:56	1.33
@@ -265,7 +265,7 @@
 			next;
 		}
 		use Bio::DB::GenBank;
-		my $gb = new Bio::DB::GenBank;
+		my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
 		my $seq = $gb->get_Seq_by_acc($acc);
 		my $length;
 		if ($seq){$length = $seq->length;}
@@ -309,7 +309,7 @@
 			next;
 		}
 		use Bio::DB::GenBank;
-		my $gb = new Bio::DB::GenBank;
+		my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
 		my $seq = $gb->get_Seq_by_acc($acc);
 		my $length;my $sequence;
 		if ($seq){$length = $seq->length;$sequence = $seq->seq}
@@ -354,7 +354,7 @@
 			next;
 		}
 		use Bio::DB::GenBank;
-		my $gb = new Bio::DB::GenBank;
+		my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
 		my $seq = $gb->get_Seq_by_gi($acc);
 		my $length;
 		if ($seq){$length = $seq->length;}
@@ -399,7 +399,7 @@
 			next;
 		}
 		use Bio::DB::GenBank;
-		my $gb = new Bio::DB::GenBank;
+		my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');
 		my $seq = $gb->get_Seq_by_gi($acc);  # get the sequence object for each gi
 		my $length;my $sequence;
 		if ($seq){$length = $seq->length;$sequence = $seq->seq}  # if it exists, get the length and sequence
@@ -460,7 +460,7 @@
 		}
 
 		use Bio::DB::GenBank;
-		my $gb = new Bio::DB::GenBank;  # now that we have a namespace and ID, we are ready to retrieve
+		my $gb = new Bio::DB::GenBank(-retrievaltype => 'io_string');  # now that we have a namespace and ID, we are ready to retrieve
 		my $seq;
 		if ($namespace_LSID eq $GB_Acc_LSID){  # if the namespace is a genbank Accession thebn
 			$seq = $gb->get_Seq_by_acc($ID);  # get the sequence object for the accession