--- a/process_raw_data.py	Sun Jan 31 11:28:30 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,386 +0,0 @@
-"""
-https://www.ncbi.nlm.nih.gov/Sequin/acc.html
-https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/?report=objectonly
-"""
-
-
-class PhageBacteriaData:
-
-	def __init__(self, dataset=None):
-		"""
-		Imports a dataset from NCBI Virus, where the columns are Phage ID, Phage Name, Bacteria Name, Bacteria ID.
-		If a phage entry does not have a bacteria associated, it is deleted
-		:param dataset:
-		"""
-		import pandas as pd
-		import json
-		self.listBacID = []
-		if dataset is None:
-			file = False
-			while not file:
-				try:
-					name = input('File name: ')
-					self.data = pd.read_csv('files/' + name, header=0, index_col=0)
-					file = True
-				except:
-					print('Couldn\'t find file')
-		else:
-			self.data = pd.read_csv('files/' + dataset, header=0, index_col=0)
-			self.data = self.data.dropna(how='any')
-			self.data = self.data[self.data['Host'] != 'unclassified bacterium']
-			index_remove = []
-			for i in range(len(self.data)):
-				if 'uncultured' in self.data.iloc[i]['Species']:
-					index_remove.append(i)
-				elif 'virus' not in self.data.iloc[i]['Species'] and 'phage' not in self.data.iloc[i]['Species']:
-					index_remove.append(i)
-			self.data = self.data.drop(self.data.index[index_remove])
-			index_remove = []
-			for i in range(len(self.data)):
-				temp = self.data['Host'][i].split(' ')
-				if len(temp) <= 1:
-					index_remove.append(i)
-			self.data = self.data.drop(self.data.index[index_remove])
-		if 'Host_ID' not in self.data.columns:
-			temp = []
-			for i in self.data.index:
-				temp.append([])
-			self.data['Host_ID'] = temp
-		try:
-			with open('files/searched_accessions', 'r') as f:
-				self.searched = json.loads(f.read())
-		except:
-			self.searched = {}
-
-	def addPhageName(self):
-		"""
-		Using the entrez service, from NCBI, for each phage the name is added, from its features.
-		:return:
-		"""
-		from Bio import Entrez
-		from Bio import SeqIO
-		Entrez.email = "pedro_araujo97@hotmail.com"
-		listNames = []
-		with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=self.data.index) as handle:
-			for seq_record in SeqIO.parse(handle, "gb"):
-				listNames.append(seq_record.annotations['organism'])
-		self.data['Species'] = listNames
-
-	def addBacteriaName(self):
-		"""
-		Using the entrez service, from NCBI, for each phage the infecting bacteria name is added, from its features.
-		:return:
-		"""
-		from Bio import Entrez
-		from Bio import SeqIO
-		Entrez.email = "pedro_araujo97@hotmail.com"
-		for phage in self.data.index:
-			with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=phage) as handle:
-				seq_record = SeqIO.read(handle, "gb")
-				try:
-					if len(seq_record.features[0].qualifiers['host'][0].split(' ')) > 2:
-						self.data.loc[phage, 'Host'] = seq_record.features[0].qualifiers['host'][0]
-				except:
-					if len(seq_record.features[0].qualifiers['lab_host'][0].split(' ')) > 2:
-						self.data.loc[phage, 'Host'] = seq_record.features[0].qualifiers['lab_host'][0]
-		self.save_data()
-
-	def addBacteriaGenome(self):
-		"""
-		For each phage, the associated scientific articles in pubmed are looked. From theses pubmed articles, all associated IDs are extracted.
-		If the ID corresponds to a bacterial strain, its accession ID is added to the Bacteria ID column.
-		:return:
-		"""
-		from Bio import Entrez
-		import ast
-		import pickle
-		from pathlib import Path
-		Entrez.email = "pedro_araujo97@hotmail.com"
-		my_file = Path("files/searched_hosts")
-		if my_file.is_file():
-			with open('files/searched_hosts', 'rb') as f:
-				list_done = pickle.load(f)
-		else:
-			list_done = []
-		count = 0
-		try:
-			for phageID in self.data.index:
-				if phageID in list_done: continue
-				listBactID = ast.literal_eval(self.data.loc[phageID, 'Host_ID'])
-				try:
-					with Entrez.elink(dbfrom='nuccore', db='pubmed', id=phageID) as handle:
-						pubmed = Entrez.read(handle)
-					for i in pubmed[0]['LinkSetDb']:
-						if 'weighted' not in i["LinkName"]:
-							for link in i["Link"]:
-								try:
-									with Entrez.elink(dbfrom='pubmed', db="nucleotide", id=link['Id']) as handle:
-										genomes = Entrez.read(handle)
-									for i in genomes[0]['LinkSetDb']:
-										if 'weighted' not in i['LinkName']:
-											for id in i['Link']:
-												with Entrez.esummary(db='nucleotide', id=id['Id']) as handle:
-													bacorg = Entrez.read(handle)
-													if bacorg[0]['Caption'] != phageID and 'phage' not in bacorg[0][
-														'Title'].lower() \
-															and bacorg[0][
-														'AccessionVersion'] not in listBactID and 'cds' not in \
-															bacorg[0]['Title'].lower() and 'shotgun' not in bacorg[0][
-														'Title'].lower():
-														if any(z in bacorg[0]['AccessionVersion'][:3] for z in
-															   ['NC_', 'AC_', 'NZ_', 'CP', 'AE', 'CY', 'AP']):
-															listBactID.append(bacorg[0]['AccessionVersion'])
-															self.searched[bacorg[0]['AccessionVersion']] = 'yes'
-															count += 1
-														elif not any(z in bacorg[0]['AccessionVersion'][:3] for z in
-																	 ['MN', 'FM', 'MQ', 'MR', 'MK', 'AB', 'MF', 'KP',
-																	  'NM_', 'KC', 'MH', 'AY', 'FN', 'AY']) \
-																and 'complete' in bacorg[0]['Title'].lower():
-															if bacorg[0]['AccessionVersion'] in self.searched.keys():
-																add = self.searched[bacorg[0]['AccessionVersion']]
-															else:
-																add = input('Check ' + bacorg[0][
-																	'AccessionVersion'] + '\nDo you wish to add it? (yes/no)')
-															if 'y' in add.lower():
-																listBactID.append(bacorg[0]['AccessionVersion'])
-																self.searched[bacorg[0]['AccessionVersion']] = 'yes'
-																count += 1
-															else:
-																self.searched[bacorg[0]['AccessionVersion']] = 'no'
-								except:
-									pass
-				except:
-					pass
-				self.data.loc[phageID, 'Host_ID'] = listBactID
-				list_done.append(phageID)
-				with open('files/searched_hosts', 'wb') as f:
-					pickle.dump(list_done, f)
-				self.save_data()
-				print(phageID)
-		except:
-			print('Bacterial host name missing. Searching from phage id')
-			pass
-		print('For future reference,', count, "new bacterial ID's were added.")
-		self.save_data()
-
-	def checkAbstracts(self):
-		"""
-		For each phage, the associated scientific articles in pubmed are looked. From theses pubmed articles, the abstracted is searched for mentions of bacterial strains.
-		If bacterial strains are found, its accession IDs are added to the Bacteria ID column.
-		:return:
-		"""
-		from Bio import Entrez
-		import re
-		import ast
-		Entrez.email = 'pedro_araujo97@hotmail.com'
-		count = 0
-		for phageID in self.data.index:
-			if len(self.data.loc[phageID, 'Host'].split()) < 3:
-				with Entrez.elink(dbfrom='nuccore', db='pubmed', id=phageID) as handle:
-					pubmed = Entrez.read(handle)
-				listBactID = ast.literal_eval(self.data.loc[phageID, 'Host_ID'])
-				for i in pubmed[0]['LinkSetDb']:
-					if 'weighted' not in i["LinkName"]:
-						for link in i["Link"]:
-							try:
-								with Entrez.efetch(db="pubmed", rettype="medline", retmode="xml",
-												   id=link['Id']) as handle:
-									article = Entrez.read(handle)
-								abstract = \
-								article['PubmedArticle'][0]['MedlineCitation']['Article']['Abstract']['AbstractText'][0]
-								x = re.findall('\w{0,1}[A-Z]{1,5}[0-9]{1,5}[-,:]{0,1}[A-Z]{0,5}[1-9]{0,5}', abstract)
-								for i in range(len(x)):
-									x[i] = x[i].strip(',;')
-								x = list(set(x))
-								for i in x:
-									if 'ORF' in i:
-										x.remove(i)
-								for strain in x:
-									with Entrez.esearch(db='nucleotide', term='((((' + self.data.loc[
-										phageID, 'Host'] + ' ' + strain + ' AND complete sequence) NOT shotgun[Title]) NOT phage[Title]) NOT cds[Title]) NOT gene[Title]',
-														idtype="acc") as handle:
-										species = Entrez.read(handle)
-										strains = species['IdList']
-										for i in strains:
-											if any(z in i for z in ['NC_', 'NZ_', 'AC_', 'CP', 'AE', 'CY',
-																	'AP']) and i not in listBactID:
-												listBactID.append(i)
-												self.searched[i] = 'yes'
-												count += 1
-											elif not any(z in i[:3] for z in
-														 ['MN', 'FM', 'MQ', 'MR', 'MK', 'AB', 'MF', 'KP', 'NM_', 'KC',
-														  'MH', 'AY', 'FN', 'AY']) and i not in listBactID:
-												if i in self.searched.keys():
-													add = self.searched[i]
-												else:
-													add = input('Check ' + i + '\nDo you wish to add it? (yes/no)')
-												if 'y' in add.lower():
-													listBactID.append(i)
-													self.searched[i] = 'yes'
-													count += 1
-												else:
-													self.searched = 'no'
-							except:
-								pass
-				self.data.loc[phageID, 'Host_ID'] = listBactID
-		print('For future reference,', count, "new bacterial ID's were added.")
-		self.save_data()
-
-	def saveAbstracts(self):
-		"""
-		For each phage, the associated scientific articles in pubmed are looked.
-		From theses pubmed articles, the abstracted is saved in a dictionary structure, where each phage ID is associated with a list of abstracts.
-		These abstracts can be used for later processing.
-		:return:
-		"""
-		from Bio import Entrez
-		import json
-		Entrez.email = 'pedro_araujo97@hotmail.com'
-		dicPhageAbstracts = {}
-
-		for phageID in self.data.index:
-			print(phageID, end='\n')
-			dicPhageAbstracts[phageID] = []
-			with Entrez.elink(dbfrom='nuccore', db='pubmed', id=phageID) as handle:
-				pubmed = Entrez.read(handle)
-			lista = []
-			for i in pubmed[0]['LinkSetDb']:
-				if 'weighted' not in i["LinkName"]:
-					for link in i["Link"]:
-						try:
-							with Entrez.efetch(db="pubmed", rettype="medline", retmode="xml", id=link['Id']) as handle:
-								article = Entrez.read(handle)
-							abstract = \
-							article['PubmedArticle'][0]['MedlineCitation']['Article']['Abstract']['AbstractText'][0]
-							dicPhageAbstracts[phageID].append([link['Id'], abstract])
-						except:
-							pass
-		with open('files/phageAbstracts.json', 'w') as f:
-			json.dump(dicPhageAbstracts, f)
-
-	def searchBacName(self):
-		from Bio import Entrez
-		import ast
-		Entrez.email = "pedro_araujo97@hotmail.com"
-		count = 0
-		for phageID in self.data.index:
-			if len(self.data.loc[phageID, 'Host'].split()) > 2:
-				listBactID = ast.literal_eval(self.data.loc[phageID, 'Host_ID'])
-				with Entrez.esearch(db='nucleotide', term='((((' + self.data.loc[
-					phageID, 'Host'] + ' AND complete sequence) NOT shotgun[Title]) NOT phage[Title]) NOT cds[Title]) NOT gene[Title]',
-									idtype="acc") as handle:
-					species = Entrez.read(handle)
-					strains = species['IdList']
-					for j in strains:
-						if any(z in j[:3] for z in
-							   ['NC_', 'NZ_', 'AC_', 'CP', 'AE', 'CY', 'AP']) and j not in listBactID:
-							listBactID.append(j)
-							self.searched[j] = 'yes'
-							count += 1
-						elif not any(z in j[:3] for z in
-									 ['MN', 'FM', 'MQ', 'MR', 'MK', 'AB', 'MF', 'KP', 'NM_', 'KC', 'MH', 'AY', 'FN',
-									  'AY']) and j not in listBactID:
-							if j in self.searched.keys():
-								add = self.searched[j]
-							else:
-								add = input('Check ' + j + '\nDo you wish to add it? (yes/no)')
-							if 'y' in add.lower():
-								listBactID.append(j)
-								self.searched[j] = 'yes'
-								count += 1
-							else:
-								self.searched[j] = 'no'
-				self.data.loc[phageID, 'Host_ID'] = listBactID
-		print('For future reference,', count, "new bacterial ID's were added.")
-		self.save_data()
-
-	def createListBacID(self, lower=0, upper=100):
-		"""
-		More sequential than previous methods. Maybe include every single one...
-		:param lower: lower index from the phage list (numeric)
-		:param upper: upper index from the phage list (numeric)
-		:return:
-		"""
-		from Bio import Entrez
-		Entrez.email = 'pedro_araujo97@hotmail.com'
-		for i in range(lower, upper):
-			phageID = self.data.index[i]
-			BactID = []
-			name = test.data.loc[phageID]['Bacteria Name']
-			try:
-				if name != 'unclassified bacterium' and not name != name:  # Verificação de hosts válidos
-					with Entrez.elink(dbfrom='nuccore', db='pubmed', id=phageID) as handle:
-						pubmed = Entrez.read(handle)
-					for link in pubmed[0]["LinkSetDb"][0]["Link"]:
-						try:
-							with Entrez.elink(dbfrom='pubmed', db="nucleotide", id=link['Id']) as handle:
-								genomes = Entrez.read(handle)
-							for id in genomes[0]['LinkSetDb'][0]['Link']:
-								with Entrez.esummary(db='nucleotide', id=id['Id']) as handle:
-									bacorg = Entrez.read(handle)
-									if 'NC_' in bacorg[0]['AccessionVersion'] or 'NZ_' in bacorg[0]['AccessionVersion']:
-										if bacorg[0]['Caption'] != phageID:
-											BactID.append(bacorg[0]['AccessionVersion'])
-						except:
-							pass
-				else:
-					pass
-			except:
-				pass
-			self.listBacID.append(BactID)
-
-	def check_bacteria(self):
-		from Bio import Entrez
-		from Bio import SeqIO
-		import ast
-		Entrez.email = "pedro_araujo97@hotmail.com"
-		all_bact = []
-		for i in self.data.index:
-			for bact in ast.literal_eval(self.data.loc[i, 'Host_ID']):
-				if bact[:-2] not in all_bact:
-					all_bact.append(bact[:-2])
-		list_remove = []
-		for bact in all_bact:
-			if bact not in list_remove:
-				try:
-					with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=bact) as handle:
-						seq_record = SeqIO.read(handle, "gb")
-					if not any(i in seq_record.description.lower() for i in ['pneumoniae', 'coli', 'baumannii']) or not any(i in seq_record.description.lower() for i in ['escherichia', 'acinetobacter', 'klebsiella']) \
-							or 'phage' in seq_record.description.lower() or 'virus' in seq_record.description.lower():
-						list_remove.append(bact)
-				except:
-					list_remove.append(bact)
-		print(list_remove)
-		for phage in self.data.index:
-			listBactID = ast.literal_eval(self.data.loc[phage, 'Host_ID'])
-			for bact in listBactID:
-				if bact[:-2] in list_remove:
-					listBactID.remove(bact)
-			self.data.loc[phage, 'Host_ID'] = listBactID
-		self.data.to_csv('files/NCBI_Phage_Bacteria_Data.csv')
-
-	def save_data(self):
-		"""
-		Saves the data in csv format.
-		:return:
-		"""
-		import json
-		self.data.to_csv('files/NCBI_Phage_Bacteria_Data.csv')
-		with open('files/searched_accessions', 'w') as f:
-			json.dump(self.searched, f)
-
-
-if __name__ == '__main__':
-	test = PhageBacteriaData('NCBI_Phage_Bacteria_Data.csv')  # sequences
-	test.addBacteriaName()
-	test.addBacteriaGenome()
-	test.searchBacName()  # 2266 bacteria added
-	test.checkAbstracts()
-	# test.data = test.data.drop(columns=['Bacteria ID'])
-	test.searchBacName()
-	# test.createListBacID(0, 100)
-	# test.data = test.data.iloc[:, 0:3]
-	test.check_bacteria()
-	test.save_data()
-# test.extractProtein()
-# test.importProtein('Phage')