[Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature NormalizedFeature.pm, 1.26, 1.27

Lincoln Stein lstein at dev.open-bio.org
Mon Feb 26 19:26:18 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature
In directory dev.open-bio.org:/tmp/cvs-serv18546/Bio/DB/SeqFeature

Modified Files:
	NormalizedFeature.pm 
Log Message:
fixed various problems with gff3_string formatting of Bio::Graphics::FeatureBase; (1) was dumping empty Alias attributes and (2) was not dumping phase 0 CDS fields

Index: NormalizedFeature.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/NormalizedFeature.pm,v
retrieving revision 1.26
retrieving revision 1.27
diff -C2 -d -r1.26 -r1.27
*** NormalizedFeature.pm	23 Feb 2007 21:53:17 -0000	1.26
--- NormalizedFeature.pm	27 Feb 2007 00:26:15 -0000	1.27
***************
*** 477,490 ****
    for my $t (@tags) {
      my @values = $self->each_tag_value($t);
!     @values = grep {$_ ne $load_id && $_ ne $target} @values if $t eq 'Alias';
      # these are hacks, which we don't want to appear in the file
      next if $t eq 'load_id';
      next if $t eq 'parent_id';
      foreach (@values) { s/\s+$// } # get rid of trailing whitespace
!     # push @result,join '=',$self->escape($t),$self->escape($_) foreach @values; 
!     # NO! Multiple attributes of the same type are indicated by
!     # separating the values with the comma "," character - per
!     # http://www.sequenceontology.org/gff3.shtml.  Do it this way:
!     push @result,join '=',$self->escape($t),join(',', map {$self->escape($_)} @values);
    }
    my $id   = $self->primary_id;
--- 477,490 ----
    for my $t (@tags) {
      my @values = $self->each_tag_value($t);
! 
!     # This line prevents Alias from showing up if it matches the load id, but this is not good
!     # @values = grep {$_ ne $load_id && $_ ne $target} @values if $t eq 'Alias';
! 
      # these are hacks, which we don't want to appear in the file
      next if $t eq 'load_id';
      next if $t eq 'parent_id';
+ 
      foreach (@values) { s/\s+$// } # get rid of trailing whitespace
!     push @result,join '=',$self->escape($t),join(',', map {$self->escape($_)} @values) if @values;
    }
    my $id   = $self->primary_id;



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