Create DDE.py

DDE.py

@@ -0,0 +1,89 @@
+import re
+import math
+from util.seed import set_seed
+import pandas as pd
+import numpy as np
+
+set_seed()
+
+def DDE(fastas, **kw):
+	AA = ['A', 'C', 'D', 'E', 'F', 'G', 'H',
+          'I', 'K', 'L', 'M', 'N', 'P', 'Q',
+          'R', 'S', 'T', 'V', 'W', 'Y']
+
+	myCodons = {
+		'A': 4,
+		'C': 2,
+		'D': 2,
+		'E': 2,
+		'F': 2,
+		'G': 4,
+		'H': 2,
+		'I': 3,
+		'K': 2,
+		'L': 6,
+		'M': 1,
+		'N': 2,
+		'P': 4,
+		'Q': 2,
+		'R': 6,
+		'S': 6,
+		'T': 4,
+		'V': 4,
+		'W': 1,
+		'Y': 2
+	}
+
+	encodings = []
+	diPeptides = [aa1 + aa2 for aa1 in AA for aa2 in AA]
+	header = ['#'] + diPeptides
+	encodings.append(header)
+
+	myTM = []
+	for pair in diPeptides:
+		myTM.append((myCodons[pair[0]] / 61) * (myCodons[pair[1]] / 61))
+
+	AADict = {}
+	for i in range(len(AA)):
+		AADict[AA[i]] = i
+
+	for i in fastas:
+		name, sequence = i[0], re.sub('-', '', i[1])
+		code = [name]
+		tmpCode = [0] * 400
+		for j in range(len(sequence) - 2 + 1):
+			tmpCode[AADict[sequence[j]] * 20 + AADict[sequence[j+1]]] = tmpCode[AADict[sequence[j]] * 20 + AADict[sequence[j+1]]] +1
+		if sum(tmpCode) != 0:
+			tmpCode = [i/sum(tmpCode) for i in tmpCode]
+
+		myTV = []
+		for j in range(len(myTM)):
+			myTV.append(myTM[j] * (1-myTM[j]) / (len(sequence) - 1))
+
+		for j in range(len(tmpCode)):
+			tmpCode[j] = (tmpCode[j] - myTM[j]) / math.sqrt(myTV[j])
+
+		code = code + tmpCode
+		encodings.append(code)
+	return encodings
+
+
+def feature_DDE(file_path):
+    f = open(file_path, 'r', encoding='utf-8')
+    fasta_list = np.array(f.readlines())
+    aa_feature_list = []
+    for flag in range(0, len(fasta_list), 2):
+        fasta_str = [[fasta_list[flag].strip('\n').strip(), fasta_list[flag + 1].strip('\n').strip()]]
+        dpc_output = DDE(fasta_str)
+        dpc_output[1].remove(dpc_output[1][0])
+        dpc_feature = dpc_output[1][:]
+        aa_feature_list.append(dpc_feature)
+    aa_feature_list = pd.DataFrame(aa_feature_list)
+    aa_feature_list = aa_feature_list.iloc[:,:]
+    coloumnname = []
+    for i in range(len(aa_feature_list.columns)):
+        x = 'DDE'+str(i+1)
+        coloumnname.append(x)
+    aa_feature_list.columns = coloumnname
+    return aa_feature_list
+