csv_diff addition command line arguments

Author: mayankmtg

csv_diff.py

@@ -0,0 +1,84 @@
+import numpy as np
+from scipy.stats.stats import pearsonr
+import sys
+
+print("Difference Parameters")
+mzdiff=0
+rtdiff=0
+corrthresh=0.99
+print("Median MZ Diff: "+ str(mzdiff))
+print("Median RT Diff: "+ str(rtdiff))
+print("Correlation Threshold: "+ str(corrthresh))
+if(len(sys.argv)<3):
+	print("python csv_diff.csv file1.csv file2.csv")
+	sys.exit(0)
+
+print("Programs gives the differences in file 2 with respect to file 1")
+file1=sys.argv[1]
+file2=sys.argv[2]
+
+
+line_array1=[]
+vec_array1=[]
+with open(file1) as f:
+	first=0
+	for line in f:
+		line=line.rstrip('\n')
+		if(first==0):
+			first=1
+			table_labels=line.split(',')
+			print("Removing Blanks")
+			continue
+		temp_array=line.split(',')
+		t=5
+		while(t!=0):
+			temp_array.remove('')
+			t-=1
+		line_array1.append(map(float,temp_array))
+		temp_array=temp_array[9:]
+		vec_array1.append(map(float,temp_array))
+
+line_array2=[]
+vec_array2=[]
+with open(file2) as f:
+	first=0
+	for line in f:
+		line=line.rstrip('\n')
+		if(first==0):
+			first=1
+			table_labels=line.split(',')
+			print("Removing Blanks")
+			continue
+		temp_array=line.split(',')
+		t=5
+		while(t!=0):
+			temp_array.remove('')
+			t-=1
+		line_array2.append(map(float,temp_array))
+		temp_array=temp_array[9:]
+		vec_array2.append(map(float,temp_array))
+
+line_array1=np.array(line_array1)
+line_array2=np.array(line_array2)
+vec_array1=np.array(vec_array1)
+vec_array2=np.array(vec_array2)
+print(vec_array1.shape)
+print(vec_array2.shape)
+reported_difference=[]
+for i in range(len(line_array2)):
+	flag=0
+	for j in range(len(line_array1)):
+		if(abs(line_array1[j][3]-line_array2[i][3])<=mzdiff and abs(line_array1[j][4]-line_array2[i][4])<=rtdiff):
+			first_corr=pearsonr(vec_array2[i],vec_array1[j])[0]
+			if(first_corr==1):
+				flag=1
+	if(flag==0):
+		reported_difference.append(line_array2[i])
+
+print(len(reported_difference))
+# for diff in reported_difference:
+# 	print(diff)
+
+
+
+

metric_euc.py

@@ -1,6 +1,7 @@
 import numpy as np
 import scipy.spatial.distance as eucd
 from scipy.stats.stats import pearsonr
+import sys
 
 line_array=[]
 vec_array=[]
@@ -12,7 +13,12 @@
 print("Median RT Diff: "+ str(rtdiff))
 print("Correlation Threshold: "+ str(corrthresh))
 table_labels=0
-with open('../csvFiles/test1.csv') as f:
+
+if(len(sys.argv)<3):
+	print("python metric_euc.py csv_file.csv duplicate_file.csv")
+	sys.exit(1)
+
+with open(sys.argv[1]) as f:
 	first=0
 	for line in f:
 		line=line.rstrip('\n')
@@ -67,7 +73,7 @@
 
 
 write_flag=0
-with open('../csvFiles/duplicates1.csv', 'w') as f:
+with open(sys.argv[2], 'w') as f:
 	f.write('duplicate_id,'+dell.join(table_labels)+'\n')
 	ind=1
 	for t in tup_duplicates: