--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prophage_finder.py	Wed Jan 27 13:50:11 2021 +0000
@@ -0,0 +1,102 @@
+import ast
+import json
+import os
+
+import pandas as pd
+
+from FeatureConstruction import *
+
+
+def phages_bact():
+	count_bacteria = 0
+	for phage in data.index:
+		if ast.literal_eval(data.loc[phage, 'Host_ID']):
+			count_bacteria += 1
+	return count_bacteria
+
+
+data = pd.read_csv('files/NCBI_Phage_Bacteria_Data.csv', header=0, index_col=0)
+
+with open('C:/Users/Pedro/Downloads/pha_in_bac_2_test.json', encoding='utf-8') as F:
+	prophage = json.loads(F.read())
+
+for bact in prophage.keys():
+	for phage in prophage[bact]:
+		if phage in data.index:
+			temp = ast.literal_eval(data.loc[phage, 'Host_ID'])
+			if bact + '.1' not in temp:
+				temp.append(bact+'.1')
+				data.loc[phage, 'Host_ID'] = str(temp)
+
+data.to_csv('files/NCBI_Phage_Bacteria_Data.csv')
+
+fc = FeatureConstruction()
+phageTails = fc.phageTails
+
+os.system('cd-hit -i files/tails.fasta -o files/cdhit')
+
+temp_cluster = []
+with open('files/cdhit.clstr', 'r') as f:
+	for line in f.readlines():
+		if '>Cluster' in line:
+			for prot in temp_cluster:
+				for phage in phageTails:
+					if prot in phageTails[phage].keys():
+						if phage in data.index:
+							temp_ref = ast.literal_eval(data.loc[ref_phage, 'Bacteria ID'])
+							temp = ast.literal_eval(data.loc[phage, 'Bacteria ID'])
+							for i in temp_ref:
+								if i not in temp:
+									temp.append(i)
+									data.loc[phage, 'Bacteria ID'] = str(temp)
+						break
+			temp_cluster = []
+		elif line[0] == '0':
+			pos_i = line.find('>') + 1
+			pos_f = line.find('...')
+			ref_prot = line[pos_i:pos_f]
+			for phage in phageTails:
+				if ref_prot in phageTails[phage].keys():
+					ref_phage = phage
+					break
+		else:
+			pos_i = line.find('>') + 1
+			pos_f = line.find('...')
+			temp_cluster.append(line[pos_i:pos_f])
+
+
+with open('files/bactDNA.json', encoding='utf-8') as F:
+	bacProt = json.loads(F.read())
+
+listDone = []
+for bact in bacProt:
+	if bact in listDone:
+		pass
+	else:
+		listDone.append(bact)
+		with open('files/temp_genome.fasta', 'w') as F:
+			F.write('>' + bact + '\n' + bacProt[bact] + '\n')
+		os.system('phigaro -f files/temp_genome.fasta --not-open -d -o files/temp_phigaro')  # Phigaro
+		with open('files/temp_phigaro.html', 'r') as Ph:
+			tempPhigaro = Ph.readlines()
+		for line in tempPhigaro:
+			if '<div class="accordion-body collapse"' in line:
+				VOGs = line[line.find('>')+1:].strip('\n').split(', ')
+				for vog in VOGs:
+					with open('files/VOG_tables/' + vog + '.txt', 'r') as f:
+						temp_phages = f.readlines()
+					for i in range(len(temp_phages)):
+						if i != 0:
+							phage = temp_phages[i].split('\t')[2]
+							if phage in data.index:
+								temp = ast.literal_eval(data.loc[phage, 'Bacteria ID'])
+								if bact not in temp:
+									temp.append(bact)
+									data.loc[phage, 'Bacteria ID'] = str(temp)
+		print('Number of phages with associated bacteria strains:', phages_bact(), end="\r")
+
+'''os.system('wget --post-file="files/temp_genome.fasta" "http://phaster.ca/phaster_api?contigs=1" -O files/temp_phaster') # Phaster
+with open('files/temp_phaster', encoding='utf-8') as F:
+	temp = json.loads(F.read())
+os.system('wget "http://phaster.ca/phaster_api?acc=' + temp['job_id'] + 'Z" -O files/temp_phaster') # servidor cheio
+os.system('PhiSpy.py files/temp_genome.fasta -o files/temp_phipsy') # Phipsy - não possível com fastas'''