[Bioperl-guts-l] bioperl-live/Bio/Tools GFF.pm,1.47,1.48

[Sheldon Mckay]

Update of /home/repository/bioperl/bioperl-live/Bio/Tools
In directory pub.open-bio.org:/tmp/cvs-serv20214/Bio/Tools

Modified Files:
	GFF.pm 
Log Message:
The script was silently broken by a change to the default behaviour of
the Bio::FeatureHolderI::get_all_SeqFeatures method.

I also:
1) made some changes to how shared exons are handled in response to
the updated GFF3 spec.
2) dealt with labelling problem in gene containment hierarchies derived from
third-party (non-refseq) annotations.

I think more testing is required.



Index: GFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/GFF.pm,v
retrieving revision 1.47
retrieving revision 1.48
diff -C2 -d -r1.47 -r1.48
*** GFF.pm	28 Dec 2004 19:21:39 -0000	1.47
--- GFF.pm	24 Mar 2005 13:03:24 -0000	1.48
***************
*** 1002,1011 ****
  	$name = 'SEQ';
      }
!     my @groups,
!     my @all_tags = $feat->all_tags;
      for my $tag ( @all_tags ) {
  	my $valuestr;	# a string which will hold one or more values 
! # for this tag, with quoted free text and 
! # space-separated individual values.
  	my @v;
  	for my $value ( $feat->each_tag_value($tag) ) {	    
--- 1002,1017 ----
  	$name = 'SEQ';
      }
! 
!     my @groups;
! 
!     # force leading ID and Parent tags
!     my @all_tags =  grep { !/ID/ && !/Parent/ } $feat->all_tags;
!     unshift @all_tags, 'Parent' if $feat->has_tag('Parent');
!     unshift @all_tags, 'ID' if $feat->has_tag('ID');
! 
      for my $tag ( @all_tags ) {
  	my $valuestr;	# a string which will hold one or more values 
!                         # for this tag, with quoted free text and 
!                         # space-separated individual values.
  	my @v;
  	for my $value ( $feat->each_tag_value($tag) ) {	    
***************
*** 1014,1019 ****
  		if ($value =~ /[^a-zA-Z0-9\,\;\=\.:\%\^\*\$\@\!\+\_\?\-]/) {
  		    $value =~ s/\t/\\t/g;	# substitute tab and newline 
! # characters
! 		    $value =~ s/\n/\\n/g;		# to their UNIX equivalents
  
  # Unescaped quotes are not allowed in GFF3
--- 1020,1025 ----
  		if ($value =~ /[^a-zA-Z0-9\,\;\=\.:\%\^\*\$\@\!\+\_\?\-]/) {
  		    $value =~ s/\t/\\t/g;	# substitute tab and newline 
!                                                 # characters
! 		    $value =~ s/\n/\\n/g;	# to their UNIX equivalents
  
  # Unescaped quotes are not allowed in GFF3