[Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph processed_transcript.pm, 1.9, 1.10

Lincoln Stein lstein at pub.open-bio.org
Mon Feb 13 15:47:46 EST 2006


Update of /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph
In directory pub.open-bio.org:/tmp/cvs-serv14681/Bio/Graphics/Glyph

Modified Files:
	processed_transcript.pm 
Log Message:
folded in Don Gilbert\'s patch that prevents exons from getting clipped to oblivion


Index: processed_transcript.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/processed_transcript.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** processed_transcript.pm	16 Apr 2005 18:44:36 -0000	1.9
--- processed_transcript.pm	13 Feb 2006 20:47:44 -0000	1.10
***************
*** 107,110 ****
--- 107,112 ----
      next if $e_left  > $o_right;
      last if $e_right < $o_left;
+     #dgg- need to skip 3prime/right utr for 1exon; end same as exon
+     last if (@unique_exons == 1 && $o_left > $e_left); #dgg- o_ is 3prime not 5
      # clip left hand side; may get clipped into oblivion!
      $first_exon->{left}  = $o_right + 1;
***************
*** 121,125 ****
      last if $e_left  > $o_right;
      # clip right hand side; may get clipped into oblivion!
!     $last_exon->{width}    = ($e_left - 1) - $last_exon->{left};
    }
  
--- 123,128 ----
      last if $e_left  > $o_right;
      # clip right hand side; may get clipped into oblivion!
!     #dgg- !! this always clips to oblivion: $last_exon->{width} = ($e_left - 1) - $last_exon->{left};
!     $last_exon->{width} = $o_left - $last_exon->{left}; #dgg-
    }
  



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