From 6883d2d2d1c7fde7e554be10a6f2e4d2960aa812 Mon Sep 17 00:00:00 2001
From: Suman Neupane <suman.neupane@uconn.edu>
Date: Fri, 26 May 2017 11:54:28 -0400
Subject: [PATCH] Delete readSeq.py

---
 readSeq.py | 69 ------------------------------------------------------
 1 file changed, 69 deletions(-)
 delete mode 100644 readSeq.py

diff --git a/readSeq.py b/readSeq.py
deleted file mode 100644
index 91c58a5..0000000
--- a/readSeq.py
+++ /dev/null
@@ -1,69 +0,0 @@
-def patterns(sequence_file):
- # 
-    import re, os, glob, itertools, fnmatch, sys, shutil
-    from itertools import combinations
-    from collections import Counter
-
-    script_dir = os.path.dirname(os.path.realpath(sys.argv[0]))
-#     path = os.path.join(script_dir, 'nexus')
-
-    genes = []
-    data = {}
-#     print 'Reading nexus files...'
-    for filename in glob.glob(os.path.join(script_dir, sequence_file)):
-
-        m = re.match('(.+).nex', os.path.basename(filename))
-        gene_name = m.group(1)
-#         print 'gene_name=', gene_name
-        genes.append(gene_name)
-        f = open(filename, 'r').read()
-
-        m = re.search('ntax\s*=\s*(\d+)', f, re.M | re.S)
-        ntax = int(m.group(1))
-#         print 'ntax=', ntax
-
-        m = re.search('nchar\s*=\s*(\d+)', f, re.M | re.S)
-        nchar = int(m.group(1))
-#         print 'nchar=', nchar
-
-        m = re.search('Matrix\s+(.+?);', f, re.M | re.S)
-        matrix = m.group(1).strip()
-        matrix_lines = matrix.split('\n')
-
-        taxon_names = []
-        sequences = {}
-        sequences_list = []
-        for line in matrix_lines:
-            parts = line.strip().split()
-            assert len(parts) == 2
-            taxon_name = parts[0]
-            sequence = parts[1]
-        
-            taxon_names.append(taxon_name)
-            sequences_list.append(sequence)
-            sequences[taxon_name] = sequence
-        
-        pattern_list = []
-    
-        k=0
-        while k < nchar:
-            site_pattern = ''
-            for i,m in enumerate(sequences_list):
-                site_pattern += m[k]
-            pattern_list.append(site_pattern)
-            k+=1
-        pattern_dict = dict()
-        for i in pattern_list:
-            pattern_dict[i] = pattern_dict.get(i, 0) + 1 
-    
-        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
-        sorted_values.sort(cmp = lambda x,y:cmp(x[1],y[1])) ###sorted according to values in alphabetical order
-    
-    return pattern_dict
-
-