--- a/evaluation.py	Fri Feb 23 10:46:41 2018 -0500
+++ b/evaluation.py	Sat Oct 27 13:23:06 2018 -0400
@@ -1,4 +1,4 @@
-#!/usr/bin/env python2
+#!/usr/bin/env python
 import glob
 from os import system
 import re
@@ -12,7 +12,7 @@
 
 fasta_dir = sys.argv[1]
 results_dir = sys.argv[2]
-dataNames = fasta_dir+"/data.names"
+dataNames = os.path.join(fasta_dir,"data.names")
 
 listOfClusters = []
 listOfHeaders = []
@@ -54,7 +54,7 @@
 numberOfClusters += 1  # 1 cluster for all unassigned seqs
 ignoreBlackList = False
 with open(dataNames, "r") as names:
-    for line in names.readlines():
+    for line in names:
         splits = line.split() 
         fullUniqeId = splits[3]
         fullHeader = ''
@@ -72,9 +72,9 @@
 
 toWrite = ""
 for i in range(len(listOfClusters)):
-    toWrite += listOfHeaders[i] + "\t" + listOfClusters[i] + '\n'
-
-with open(results_dir+"/fullTab.tabular", "w") as full:
+    toWrite += "%s\t%s\n" % (listOfHeaders[i], listOfClusters[i]) 
+ 
+with open(os.path.join(results_dir,"fullTab.tabular"), "w") as full:
     full.write(toWrite)
 
 
@@ -88,7 +88,11 @@
     adjusted_mutual_info_score = metrics.adjusted_mutual_info_score(listOfHeaders, listOfClusters)
     v_measure_score = metrics.v_measure_score(listOfHeaders, listOfClusters)
 
-    toWrite = "completeness_score : " + str(completeness_score) + "\n" + "homogeneity_score : " + str(homogeneity_score) + "\n" + "adjusted_rand_score : " +str(adjusted_rand_score)  + "\n" + "adjusted_mutual_info_score : " + str(adjusted_mutual_info_score)+ "\n" + "v_measure_score : " + str(v_measure_score)
+    toWrite = "completeness_score : {}\n".format(completeness_score) 
+    toWrite += "homogeneity_score : {}\n".format(homogeneity_score) 
+    toWrite += "adjusted_rand_score : {}\n".format(adjusted_rand_score)
+    toWrite += "adjusted_mutual_info_score : {}\n".format(adjusted_mutual_info_score)
+    toWrite += "v_measure_score : {}\n".format(v_measure_score)
 
 
 else: