# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1389299081 21600
# Node ID 359addb9b9d4c3c952310be84fde727099bea815
# Parent  639ee511d5522824834512db573fc91290b74ce6
Do not include the stop codon when filtering

diff -r 639ee511d552 -r 359addb9b9d4 translate_bed_sequences.py
--- a/translate_bed_sequences.py	Thu Jan 09 09:47:50 2014 -0600
+++ b/translate_bed_sequences.py	Thu Jan 09 14:24:41 2014 -0600
@@ -100,9 +100,8 @@
           tstop = len(translation)
           if not untrimmed:
             tstart = translation.rfind('*',0,junc) + 1
-            tstop = translation.find('*',junc) + 1
-            rtrim = tstop if tstop == 0 else len(translation) - tstop 
-            tstop = tstop if tstop else len(translation)
+            stop = translation.find('*',junc)
+            tstop = stop if stop >= 0 else len(translation)
           if filtering and tstart > ignore:
             continue
           trimmed = translation[tstart:tstop]
diff -r 639ee511d552 -r 359addb9b9d4 translate_bed_sequences.xml
--- a/translate_bed_sequences.xml	Thu Jan 09 09:47:50 2014 -0600
+++ b/translate_bed_sequences.xml	Thu Jan 09 14:24:41 2014 -0600
@@ -29,7 +29,7 @@
   #end if
   #if $trim.trimseqs == 'no':
     --untrimmed
-    #if $trim.max_stop_codons != None:
+    #if $trim.max_stop_codons.__str__ != '':
       --max_stop_codons $trim.max_stop_codons
     #end if
   #end if