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analytical_code/features.py

+#!/usr/bin/env python
+#_*_coding:utf-8_*_
+import argparse
+import re
+from collections import Counter
+import numpy
+import itertools
+
+def readFasta(file):
+	with open(file) as f:
+		records = f.read()
+	if re.search('>', records) == None:
+		print('The input file seems not in fasta format.')
+		sys.exit(1)
+	records = records.split('>')[1:]
+	myFasta = []
+	for fasta in records:
+		array = fasta.split('\n')
+		name, sequence = array[0].split()[0], re.sub('[^ARNDCQEGHILKMFPSTWYV-]', '-', ''.join(array[1:]).upper())
+		myFasta.append([name, sequence])
+	return myFasta
+
+def AAC(fastas):
+	AA='ACDEFGHIKLMNPQRSTVWY'
+	encodings = []
+	header=['#']
+	for i in AA:
+		header.append(i)
+	encodings.append(header)	
+	for i in fastas:
+		name, sequence = i[0], re.sub('-', '', i[1])
+		count = Counter(sequence)
+		for key in count:
+			count[key] = count[key]/len(sequence)
+		code = [name]
+		for aa in AA:
+			code.append(count[aa])
+		encodings.append(code)
+	return encodings
+
+def DPC(fastas):
+	AA = 'ACDEFGHIKLMNPQRSTVWY'
+	encodings = []
+	diPeptides = [aa1 + aa2 for aa1 in AA for aa2 in AA]
+	header = ['#'] + diPeptides
+	encodings.append(header)
+
+	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]
+		code = code + tmpCode
+		encodings.append(code)
+	return encodings
+
+def savetsv(encodings, file = 'encoding.tsv'):
+	with open(file, 'w') as f:
+		if encodings == 0:
+			f.write('Descriptor calculation failed.')
+		else:
+			for i in range(len(encodings[0]) -1):
+				f.write(encodings[0][i] + '\t')
+			f.write(encodings[0][-1] + '\n')
+			for i in encodings[1:]:
+				f.write(i[0] + '\t')
+				for j in range(1, len(i) - 1):
+					f.write(str(float(i[j])) + '\t')
+				f.write(str(float(i[len(i)-1])) + '\n')
+	return None
+
+
+import collections 
+def merge(lst1, lst2): 
+	return [(sub + [lst2[i][-1]]) for i, sub in enumerate(lst1)] 
+       
+	
+if __name__ == "__main__":
+	parser = argparse.ArgumentParser(description='Process fasta input with random forest virulence prediction model')
+	parser.add_argument("--file", required=True, help="input fasta file")
+	parser.add_argument("--out", dest='outFile',
+						help="the generated descriptor file")
+	args = parser.parse_args()
+	
+	fastas = readFasta(args.file)
+	encodings = AAC(fastas)
+	outFile = args.outFile if args.outFile != None else 'encoding.tsv'
+	savetsv(encodings, outFile)
+
+
+
+