[Bioperl-guts-l] bioperl-live/Bio/DB GFF.pm,1.130,1.131

Lincoln Stein lstein at pub.open-bio.org
Sat Jul 30 21:03:45 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio/DB
In directory pub.open-bio.org:/tmp/cvs-serv15652/Bio/DB

Modified Files:
	GFF.pm 
Log Message:
improved loading status messages and made it possible for bp_load_gff.pl to create new databases when given the -c flag


Index: GFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/GFF.pm,v
retrieving revision 1.130
retrieving revision 1.131
diff -C2 -d -r1.130 -r1.131
*** GFF.pm	29 Jul 2005 17:52:33 -0000	1.130
--- GFF.pm	31 Jul 2005 01:03:43 -0000	1.131
***************
*** 2332,2339 ****
      }
  
-     $count++;
-     print STDERR $count," features loaded$lineend" if $self->{__verbose__} && $count % 1000 == 0;
- 
      if (/^\#\#\s*sequence-region\s+(\S+)\s+(\d+)\s+(\d+)/i) { # header line
        $self->load_gff_line(
  			   {
--- 2332,2337 ----
      }
  
      if (/^\#\#\s*sequence-region\s+(\S+)\s+(\d+)\s+(\d+)/i) { # header line
+       $count++;
        $self->load_gff_line(
  			   {
***************
*** 2358,2361 ****
--- 2356,2360 ----
  
      next if /^\#/;
+ 
      my ($ref,$source,$method,$start,$stop,$score,$strand,$phase,$group) = split "\t";
      next unless defined($ref) && defined($method) && defined($start) && defined($stop);
***************
*** 2364,2367 ****
--- 2363,2369 ----
      }
  
+     $count++;
+     print STDERR $count," records$lineend" if $self->{__verbose__} && $count % 1000 == 0;
+ 
      my ($gclass,$gname,$tstart,$tstop,$attributes) = $self->split_group($group,$self->{gff3_flag});
  
***************
*** 2401,2405 ****
    }
  
!   print STDERR "\n",$count," features loaded\n" if $self->{__verbose__};
    my $result = $self->finish_load();
    $result += $self->load_sequence($io_handle,$fasta_sequence_id)
--- 2403,2407 ----
    }
  
!   print STDERR $count," records loaded\n" if $self->{__verbose__};
    my $result = $self->finish_load();
    $result += $self->load_sequence($io_handle,$fasta_sequence_id)



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