From fbf6075da209b564df7d8ae4b6f5632a1bc60a4e Mon Sep 17 00:00:00 2001 From: Suman Neupane Date: Fri, 21 Apr 2017 18:49:31 -0400 Subject: [PATCH] script that reads nexus file --- readseq.py | 18 +----------------- 1 file changed, 1 insertion(+), 17 deletions(-) diff --git a/readseq.py b/readseq.py index 75bdb56..54fb688 100644 --- a/readseq.py +++ b/readseq.py @@ -41,17 +41,11 @@ 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 @@ -59,28 +53,18 @@ def patterns(): 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