[Bioperl-guts-l] bioperl-live/Bio/Tools GFF.pm,1.53,1.54

Scott Cain scain at dev.open-bio.org
Fri Jun 16 15:22:23 EDT 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Tools
In directory dev.open-bio.org:/tmp/cvs-serv2033

Modified Files:
	GFF.pm 
Log Message:
adding items to escape in GFF3 attributes per Robert Buels patch


Index: GFF.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tools/GFF.pm,v
retrieving revision 1.53
retrieving revision 1.54
diff -C2 -d -r1.53 -r1.54
*** GFF.pm	16 Jun 2006 14:12:54 -0000	1.53
--- GFF.pm	16 Jun 2006 19:22:21 -0000	1.54
***************
*** 1026,1030 ****
  #		    $value = '"' . $value . '"';
  		}
! 		$value =~ s/([\t\n\=;,])/sprintf("%%%X",ord($1))/ge;
  	    } else {
  		# if it is completely empty, 
--- 1026,1030 ----
  #		    $value = '"' . $value . '"';
  		}
! 		$value =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge;
  	    } else {
  		# if it is completely empty, 
***************
*** 1048,1052 ****
  
          my $target_id = $origfeat->feature1->seq_id;
!         $target_id =~ s/([\t\n\=;,])/sprintf("%%%X",ord($1))/ge;    
       
  	push @groups, sprintf("Target=%s %d %d", 
--- 1048,1052 ----
  
          my $target_id = $origfeat->feature1->seq_id;
!         $target_id =~ s/([\t\n\r%&\=;,])/sprintf("%%%X",ord($1))/ge;    
       
  	push @groups, sprintf("Target=%s %d %d", 



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