script that reads nexus file

readseq.py

@@ -41,46 +41,30 @@ def patterns():
             assert len(parts) == 2
             taxon_name = parts[0]
             sequence = parts[1]
-    #         print 'sequence===', sequence
 
             taxon_names.append(taxon_name)
             sequences_list.append(sequence)
             sequences[taxon_name] = sequence
 
-
-
-    #     print 'sequences dict==', sequences
-#         print 'sequences list==', sequences_list
-
         pattern_list = []
 
         k=0
         while k < nchar:
             site_pattern = ''
             for i,m in enumerate(sequences_list):
                 site_pattern += m[k]
-    #         print 'site_pattern=', site_pattern 
             pattern_list.append(site_pattern)
             k+=1
-#         print '!!!!!!!!'
-#         print pattern_list
-#         print 
         pattern_dict = dict()
         for i in pattern_list:
-            pattern_dict[i] = pattern_dict.get(i, 0) + 1 #http://www.pythonlearn.com/html-008/cfbook010.html#
+            pattern_dict[i] = pattern_dict.get(i, 0) + 1 
 
-#         print'------------'
-#         print pattern_dict 
-#         print
         tmp = []
         for key in pattern_dict.keys(): ###convert dict to key of tupules
 #             print 'key=', key
             tmp.append((pattern_dict[key],key))
 
         sorted_values = sorted(tmp) ###sorted according to key smaller to larger
-#         print sorted_values
-#         print '**********'
-    #     sorted_values.reverse() ###sorted according to key values larger to smaller
         sorted_values.sort(cmp = lambda x,y:cmp(x[1],y[1])) ###sorted according to values in alphabetical order
 #         print sorted_values