[Gmod-gbrowse-cmts] Generic-Genome-Browser/conf/plugins GFFDumper.pm,1.21,1.22

[<she...@us...>]

Update of /cvsroot/gmod/Generic-Genome-Browser/conf/plugins
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20487

Modified Files:
	GFFDumper.pm 
Log Message:
Amputated mangled GFF2.5 appendage.


Index: GFFDumper.pm
===================================================================
RCS file: /cvsroot/gmod/Generic-Genome-Browser/conf/plugins/GFFDumper.pm,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** GFFDumper.pm	22 Feb 2004 20:28:57 -0000	1.21
--- GFFDumper.pm	2 Mar 2004 07:10:26 -0000	1.22
***************
*** 51,55 ****
  			  -values => [2,2.5,3],
  			  -labels => { 2   => '2',
! 				       2.5 => '2 (Artemis)*',
  				       3   => '3'},
  			  -default => $current_config->{version},
--- 51,55 ----
  			  -values => [2,2.5,3],
  			  -labels => { 2   => '2',
!                                        2.5 => '2.5*',
  				       3   => '3'},
  			  -default => $current_config->{version},
***************
*** 76,86 ****
  			));
    autoEscape(1);
!   $html .= p(sup('*'),
! 	     "Note: Artemis GFF will contain the ENTIRE annotated sequence. Do NOT run this on whole chromosomes!") .
! 		 p(sup('**'),
! 		   "To edit, install a helper application for MIME type",
! 		   cite('application/x-gff2'),'or',
! 		   cite('application/x-gff3')
! 		   );
    $html;
  }
--- 76,94 ----
  			));
    autoEscape(1);
! 
!   my $href = a( {-href => 'javascript:void(0)', -onclick => "alert('" .
! 		"\\'Target\\' syntax in the group field:\\n" .
!                 "GFF2:   Target class:name start stop\\n" .
! 		"GFF2.5: Target class:name ; tstart start ; tstop stop\\n')"},
! 		"similarity target" );
! 
!   $html .= p(sup('*'), 
!               "GFF2.5 is GFF2 with a special syntax for $href"
!               ) .
!            p(sup('**'),
! 	      "To edit, install a helper application for MIME type",
! 	      cite('application/x-gff2'),'or',
! 	      cite('application/x-gff3')
! 	      );
    $html;
  }
***************
*** 111,116 ****
                        $db->segment($segment->ref);
    my $coords        = $config->{coords};
-   $mode             = 'all'      if $version == 2.5;
-   $coords           = 'absolute' if $version == 2.5;
  
    $segment->refseq($segment) if $coords eq 'relative';
--- 119,122 ----
***************
*** 132,161 ****
    my @feats = ();
  
!   if ( $version == 2.5 ) {
!     # don't want aggregate features
!     @feats = $whole_segment->features;
!     $self->mangle_and_dump(\@feats,$whole_segment);
!     my $seq = $whole_segment->seq;
!     $seq  ||= ('N' x $whole_segment->length);
!     $seq    =~ s/\S{60}/$&\n/g;
!     print $seq, "\n";
!   }
!   else {
!     my $iterator = $segment->get_seq_stream(@args);
!     while ( my $f = $iterator->next_seq ) {
!       $self->print_feature($f,$version);
!     }
!   }
  
!   for my $set (@more_feature_sets) {
!     if ( $set->can('get_seq_stream') ) {
!       my @feats = ();
!       my $iterator = $set->get_seq_stream;
!       while ( my $f = $iterator->next_seq ) {
! 	$self->print_feature($f);
        }
      }
    }
- 
  }
  
--- 138,155 ----
    my @feats = ();
  
!   my $iterator = $segment->get_seq_stream(@args);
!   while ( my $f = $iterator->next_seq ) {
!     $self->print_feature($f,$version);
  
!     for my $set (@more_feature_sets) {
!       if ( $set->can('get_seq_stream') ) {
!         my @feats = ();
!         my $iterator = $set->get_seq_stream;
!         while ( my $f = $iterator->next_seq ) {
! 	  $self->print_feature($f);
!         }
        }
      }
    }
  }
  
***************
*** 175,225 ****
  }
  
- # used only for Artemis GFF 2.5
- sub mangle_and_dump {
-   my ($feats,$segment) = @_;
-   my (@gff,%seen);
-   for my $f ( @$feats ) {
-     $f->version(2.5);
-     my $s = $f->gff_string(1); # the flag is for GFF3 subfeature recursion
-     chomp $s;
-     push @gff, $s;
-     for my $ss ($f->sub_SeqFeature) {
-       # next if $ss eq $f;
-       my $s = $ss->gff_string;
-       push @gff, $s;
-     }
-   }
- 
-   # out of range features break Artemis (some kind of off by one error?)
-   my $len = $segment->length - 1;
-   for ( @gff ) {
-     my $num = (split)[4];
-     s/$num/$len/ if $num > $len;
-   }
- 
-   # sigh... Artemis mangles uppercase 'Note' attributes
-   @gff = grep { s/Note/note/g; chomp($_); $_; } @gff;
-   print join "\n", 
-     map  { $_->[3] }
-       # sort first asc. by start, then desc. by stop, then ascibetically 
-       sort { $a->[0] <=> $b->[0] or
- 	       $b->[1] <=> $a->[1] or
- 		 lc $a->[2] cmp lc $b->[2] }
- 	map  { [ (split)[3], (split)[4], (split)[2], $_ ] } @gff;
-   print "\n";
- }
- 
- sub gff25_string {
-     my ($self, $f)  = @_;
-     return 0 if $f->primary_tag =~ /component/i;
-     
-     $f->{version} = 2.5;
-     my $gff = $f->gff_string;
-     
-     # convert embedded ';' to ',' 
-     $gff =~ s/\"([^\"]);([^\"])\"/$1,$2/g;
-     $gff;
- }
- 
- 
  1;
--- 169,171 ----