Add existing file

Author: jithin8mathew

MANIFEST.in

@@ -0,0 +1 @@
+include *.txt

discere/discere.py

@@ -1,21 +1,21 @@
 import subprocess
 import sys
 from process_fasta import process_fasta
-
+from feature_extraction import feature_extraction
 system = sys.platform
 
-def feat_ext():
-	print("Extracting features....")
-	if system == 'linux':
-		subprocess.run(['python3','feature_extraction.py'])
-	else:
-		subprocess.run(['python.exe','process_fasta.py'])
+# def feat_ext():
+# 	print("Extracting features....")
+# 	if system == 'linux':
+# 		subprocess.run(['python3','feature_extraction.py'])
+# 	else:
+# 		subprocess.run(['python.exe','process_fasta.py'])
 
-def extract_feature(positive, negative):
+def extract_feature(positive, negative, outdir):
 	code = process_fasta(positive, negative)
 	if code is True:
 		try:
-			feat_ext()
+			feature_extraction(outdir)
 		except Exception:
 			print('Failed to extract feautres... \n Code exiting with incomplete termination...')
 	else:print('Error processing the fasta files !')

discere/feature_extraction.py

@@ -4,44 +4,45 @@
 import pandas as pd
 from Bio.SeqUtils.ProtParam import ProteinAnalysis
 
-path_=os.getcwd()		# get the current working directory
-_=(os.path.join(path_,"data/data.txt"))		# path to input data (sequence) folder
-
-print('Reading data...')
-if os.path.exists(_):data=pd.read_table(_)		#read the file as Pandas DataFrame
-print('Clearing existing files...')
-try:[os.remove(filenames[0]+x) for filenames in os.walk(path_+'/data/') for x in (filenames[2])]		# remove the file if already exist
-except Exception:pass
-
-seq_list, cls_list=data['sequence'].tolist(), data['class'].tolist() # get the sequence and class to lists
-
-pth=(path_+"/output/")
-if not os.path.exists(pth):os.makedirs(pth)
-
-try:[os.remove(filenames[0]+x) for filenames in os.walk(pth) for x in (filenames[2])]		# remove the file if already exist
-except Exception:pass
-
-attr=open(path_+"/config/attrib","rb")
-attr=pickle.load(attr)		# load the pickle file with attribue names (for weka)
-with open(pth+"/weka_output.arff","a+") as wk: wk.write("".join('{}\n'.format(x) for x in attr))
-
-def format_output(aa_count,cnt):				 # write the extracted feature values to arff (weka), txt(svm) and csv file
-	a=(dict(zip(it.count(), list(aa_count.values()))))
-	if cnt==1:
-		with open(pth+"svm_out.txt","a+")as s: s.write("+1 "+' '.join("{}:{}".format(k, v) for k, v in a.items())+"\n")
-		with open(pth+"weka_output.arff","a+") as w: w.write(' '.join("{},".format(x) for x in list(aa_count.values()))+" serk\n")
-		with open(pth+"tain_DL.csv","a+") as DPL: DPL.write(''.join("{},".format(x) for x in list(aa_count.values()))+str(round(aromat,3))+","+str(round(fraction[0],3))+","+str(round(fraction[1],3))+","+str(round(fraction[2],3))+","+str(round(iso,3))+","+str(mol_w)+","+str(ins)+","+str(cnt)+"\n")
-	else:
-		with open(path_+"svm_out.txt","a+")as s:s.write("-1 "+' '.join("{}:{}".format(k, v) for k, v in a.items())+"\n")
-		with open(pth+"weka_output.arff","a+") as w: w.write(' '.join("{},".format(x) for x in list(aa_count.values()))+" loc\n")
-		with open(pth+"tain_DL.csv","a+") as DPL: DPL.write(''.join("{},".format(x) for x in list(aa_count.values()))+str(round(aromat,3))+","+str(round(fraction[0],3))+","+str(round(fraction[1],3))+","+str(round(fraction[2],3))+","+str(round(iso,3))+","+str(mol_w)+","+str(ins)+","+"0"+"\n")
-
-for seq,cl in zip(seq_list,cls_list):		# main loop to extract the features
-	_= ProteinAnalysis(seq)					# Biopython protein analysis package
-	aa_count=(_.count_amino_acids())		# amino acid count
-	aromat, fraction, iso=_.aromaticity(), _.secondary_structure_fraction(), _.isoelectric_point()
-	try:mol_w, ins=("%0.2f" % _.molecular_weight()),("%0.2f" %_.instability_index())
-	except Exception:mol_w,ins= mol_w,ins	# aromaticity, sec_strucure_fraction, iso_electric point , molecular weight, instability index
-	format_output(aa_count,cl)
-print("Feature extraction complete...")
-print("Extracted features are saved in data/output directory in .txt, .arff and .csv formats")
+def feature_extraction(outdir):
+	path_=os.getcwd()		# get the current working directory
+	_=(os.path.join(path_,"data/data.txt"))		# path to input data (sequence) folder
+
+	print('Reading data...')
+	if os.path.exists(_):data=pd.read_table(_)		#read the file as Pandas DataFrame
+	print('Clearing existing files...')
+	try:[os.remove(filenames[0]+x) for filenames in os.walk(path_+'/data/') for x in (filenames[2])]		# remove the file if already exist
+	except Exception:pass
+
+	seq_list, cls_list=data['sequence'].tolist(), data['class'].tolist() # get the sequence and class to lists
+
+	pth=outdir+'/'
+	if not os.path.exists(pth):os.makedirs(pth)
+
+	try:[os.remove(filenames[0]+x) for filenames in os.walk(pth) for x in (filenames[2])]		# remove the file if already exist
+	except Exception:pass
+
+	attr=open(path_+"/config/attrib","rb")
+	attr=pickle.load(attr)		# load the pickle file with attribue names (for weka)
+	with open(pth+"/weka_output.arff","a+") as wk: wk.write("".join('{}\n'.format(x) for x in attr))
+
+	def format_output(aa_count,cnt):				 # write the extracted feature values to arff (weka), txt(svm) and csv file
+		a=(dict(zip(it.count(), list(aa_count.values()))))
+		if cnt==1:
+			with open(pth+"svm_out.txt","a+")as s: s.write("+1 "+' '.join("{}:{}".format(k, v) for k, v in a.items())+"\n")
+			with open(pth+"weka_output.arff","a+") as w: w.write(' '.join("{},".format(x) for x in list(aa_count.values()))+" serk\n")
+			with open(pth+"tain_DL.csv","a+") as DPL: DPL.write(''.join("{},".format(x) for x in list(aa_count.values()))+str(round(aromat,3))+","+str(round(fraction[0],3))+","+str(round(fraction[1],3))+","+str(round(fraction[2],3))+","+str(round(iso,3))+","+str(mol_w)+","+str(ins)+","+str(cnt)+"\n")
+		else:
+			with open(path_+"svm_out.txt","a+")as s:s.write("-1 "+' '.join("{}:{}".format(k, v) for k, v in a.items())+"\n")
+			with open(pth+"weka_output.arff","a+") as w: w.write(' '.join("{},".format(x) for x in list(aa_count.values()))+" loc\n")
+			with open(pth+"tain_DL.csv","a+") as DPL: DPL.write(''.join("{},".format(x) for x in list(aa_count.values()))+str(round(aromat,3))+","+str(round(fraction[0],3))+","+str(round(fraction[1],3))+","+str(round(fraction[2],3))+","+str(round(iso,3))+","+str(mol_w)+","+str(ins)+","+"0"+"\n")
+
+	for seq,cl in zip(seq_list,cls_list):		# main loop to extract the features
+		_= ProteinAnalysis(seq)					# Biopython protein analysis package
+		aa_count=(_.count_amino_acids())		# amino acid count
+		aromat, fraction, iso=_.aromaticity(), _.secondary_structure_fraction(), _.isoelectric_point()
+		try:mol_w, ins=("%0.2f" % _.molecular_weight()),("%0.2f" %_.instability_index())
+		except Exception:mol_w,ins= mol_w,ins	# aromaticity, sec_strucure_fraction, iso_electric point , molecular weight, instability index
+		format_output(aa_count,cl)
+	print("Feature extraction complete...")
+	print("Extracted features are saved in" +outdir + "/ directory in .txt, .arff and .csv formats")