--- a/weblogolib/__init__.py	Mon Jan 16 07:03:36 2012 -0500
+++ b/weblogolib/__init__.py	Fri Jan 20 09:03:40 2012 -0500
@@ -132,6 +132,7 @@
 altype="codonsT"
 offset=0
 isreversed=False
+show_warnings=False
 col=[]
 
 
@@ -169,7 +170,7 @@
 
 description  = "Create sequence logos from biological sequence alignments." 
 
-__version__ = "1.0"
+__version__ = "1.1"
 
 # These keywords are subsituted by subversion.
 # The date and revision will only  tell the truth after a branch or tag,
@@ -312,9 +313,9 @@
 # Check that can get 80 characters in journal page @small
 # 40 chacaters in a journal column
 std_sizes = {
-    "small" : LogoSize( stack_width = 10, stack_height = 10*1*5), 
-    "medium" : LogoSize( stack_width = 10*2, stack_height = 10*2*5),
-    "large"  : LogoSize( stack_width = 10*3, stack_height = 10*3*5),    
+    "small" : LogoSize( stack_width = 16.2, stack_height = 10*1*5), 
+    "medium" : LogoSize( stack_width = 16.2*2, stack_height = 10*2*5),
+    "large"  : LogoSize( stack_width = 16.2*3, stack_height = 10*3*5),    
 }
             
             
@@ -439,6 +440,7 @@
         self.yaxis_scale = None
 
         self.show_xaxis = True
+        self.strict=False
         self.xaxis_label = ""
         self.xaxis_tic_interval =1
         self.rotate_numbers = False
@@ -798,7 +800,7 @@
         "errorbar_width_fraction",
         "errorbar_gray",    "small_fontsize",       "fontsize",
         "title_fontsize",   "number_fontsize",      "text_font",
-        "logo_font",        "title_font",          
+        "logo_font",        "title_font",           "strict",
         "logo_label",       "yaxis_scale",          "end_type",
         "debug",            "show_title",           "show_xaxis",
         "show_xaxis_label", "show_yaxis",           "show_yaxis_label",
@@ -930,6 +932,8 @@
 
     # Create and output logo
     template = resource_string( __name__, 'template.eps', __file__)
+    
+
     logo = Template(template).substitute(subsitutions)
     print >>fout, logo
  
@@ -1248,6 +1252,14 @@
               if len(str(seqs[i][(counter):(counter+3)]))==3 and len(seqs[i][(counter):(counter+3)].strip("GATUC"))==0  :
 		if(str(seqs[i][(counter):(counter+3)]) in alphabet):
                   x[counter/3][ (alphabet.index(str(seqs[i][(counter):(counter+3)]))) ]+=1
+              elif show_warnings:
+		if len(seqs[i][(counter):(counter+3)].strip("GATUC"))==1 or len(seqs[i][(counter):(counter+3)].strip("GATUC"))==2 :
+		  print >>sys.stderr, 'Warning:Incomplete or non GATUC codon detected:', seqs[i][(counter):(counter+3)]
+		  print >>sys.stderr, 'Position:',counter
+		  print >>sys.stderr, 'Sequence:',i
+		  print >>sys.stderr, 'This will be treated as ---'
+
+
 	    counter=counter+3
 	  counts=asarray(x)
         else:
@@ -1369,12 +1381,19 @@
       if not line:
         break
       line = line.split()
-      priordict[line[0]]=line[1]
-    return priordict    
+      
+      if(altype=="codonsT"):
+	priordict[line[0].upper().replace("U", "T")]=(float(line[1])/1000)*64
+      else:
+	priordict[line[0].upper().replace("T", "U")]=(float(line[1])/1000)*64
+
+    return priordict
 
 def _build_logodata(options) :
     global offset
     offset=options.frame
+    global show_warnings
+    show_warnings = options.strict
     options.alphabet = None
     options.ignore_lower_case = False
     #options.default_color = Color.by_name("black")
@@ -1384,7 +1403,7 @@
     seqs = read_seq_data(options.fin, 
         options.input_parser.read,
         alphabet=options.alphabet,
-        ignore_lower_case = options.ignore_lower_case)      
+        ignore_lower_case = options.ignore_lower_case)    
     if(options.priorfile!=None):
       if(altype=="CodonsT"):
         options.composition= str(read_priors(options.priorfile,codon_alphabetT))
@@ -1408,6 +1427,7 @@
         "logo_title",
         "yaxis_label", 
         "show_xaxis",
+        "strict",
         "show_yaxis",        
         "xaxis_label", 
         "show_ends",
@@ -1644,7 +1664,13 @@
         type="int",
         help="Upper bound of sequence to display",
         metavar="INDEX")
-
+        
+    data_grp.add_option( "-G", "--strict",
+        dest="strict",
+        action="store",
+        type="boolean",
+        help="Issue warnings if partial codons are encountered. Default: %default",default = defaults.strict,
+        metavar="True/False")
     # ========================== FORMAT OPTIONS ==========================
 
     format_grp.add_option( "-s", "--size",