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Author: hani-girgis

makePhylipMatrix.py

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+#
+# Author: Hani Z. Girgis, PhD
+#
+#
+# Purpose: This program converts all-versus-all identity scores produced 
+# by Identity to Phylip distance matrix
+# Requirements: Python 3 with NumPy.
+#
+
+import numpy as np
+import sys
+
+   
+def make_matrix(file_in, file_out):    
+    file = open(file_in, 'r')
+    # List of labels
+    label_dict = {}
+    seq_index = 0
+    for line in file:
+        token_list = line.strip().split("\t")
+         
+        if not token_list[0] in label_dict:
+            label_dict[token_list[0]] = seq_index
+            seq_index += 1
+         
+        if not token_list[1] in label_dict:    
+            label_dict[token_list[1]] = seq_index
+            seq_index += 1
+ 
+    label_count = len(label_dict.keys())
+ 
+    # The matrix 
+    matrix = np.ones((label_count, label_count))
+    
+    # Identity does not report the sequence versus itself
+    for i in range(0, label_count):
+        matrix[i][i] = 0.00000000
+            
+    # Go to the begining of the file
+    file.seek(0)
+    for line in file:
+        token_list = line.strip().split("\t")
+        distance = 1.0 - float(token_list[2])
+ 
+        if(distance < 0.0):
+            distance = 0.0
+        elif(distance > 1.0):
+            distance = 1.0
+ 
+        id_1 = label_dict[token_list[0]]
+        id_2 = label_dict[token_list[1]]
+        matrix[id_1][id_2] = distance
+        matrix[id_2][id_1] = distance
+      
+    file.close()
+ 
+    # Write Phylip matrix
+    sorted_key_list = sorted(label_dict.keys(), key=lambda key: label_dict[key])
+    with open(file_out, 'w') as file_object:
+        file_object.write(str(label_count) + '\n')
+        for key in sorted_key_list:
+            t = list()
+            i = label_dict[key]
+            for j in range(0, label_count):
+                t.append(str.format('{0:.8f}', matrix[i][j])) #round(matrix[i][j], 8))
+            s = ' '    
+            t = [str(x) for x in t]
+            # End a species name with \t
+            file_object.write(key[1:] + '\t' + s.join(t) + '\n')
+
+if len(sys.argv) != 3:
+    print("Use: python3 ", sys.argv[0], "allVsAllIdentityFile outputFileName")
+    print()
+    print("Please provide an all-versus-all file produced by Identity and an output file name.")
+    print()
+    print("Example: python3 " + sys.argv[0] + " all_vs_all_identity_scores matrix.phylip")
+    print()
+else:
+    make_matrix(sys.argv[1], sys.argv[2])