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2 class PhageBacteriaInformation:
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3
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4 def __init__(self, dataset=None):
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5 """
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6 Imports a dataset from NCBI Virus, where the columns are Phage ID, Phage Name, Bacteria Name, Bacteria ID.
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7 If a phage entry does not have a bacteria associated, it is deleted
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8 :param dataset:
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9 """
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10 import pandas as pd
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11 import ast
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12 self.phagesProteins = {}
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13 # self.phagesDNA = {}
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14 self.bactProteins = {}
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15 # self.bactDNA = {}
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16 self.data = pd.read_csv('files/'+dataset, header=0, index_col=0)
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17 self.data = self.data.dropna(how='any')
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18 self.data = self.data[self.data['Host_ID'] != '[]']
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19 index_remove = []
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20 for i in range(len(self.data)):
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21 temp = self.data['Host'][i].split(' ')
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22 if len(temp) <= 1:
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23 index_remove.append(i)
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24 self.data = self.data.drop(self.data.index[index_remove])
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25 self.all_bact = []
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26 for i in self.data.index:
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27 for bact in ast.literal_eval(self.data.loc[i, 'Host_ID']):
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28 if bact[:-2] not in self.all_bact:
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29 self.all_bact.append(bact[:-2])
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30 self.data.to_csv('files/Filtered_Phage_Bacteria.csv')
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31
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32 def addFeatures(self):
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33 """
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34 For each phage in the data, it saves its DNA sequence and all proteins, as provided by NCBI. It saves them into two variables
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35 Each bacteria associated with the phage is also searched for its DNA and proteins sequences.
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36 :return:
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37 """
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38 from Bio import Entrez
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39 from Bio import SeqIO
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40 import json
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41 import ast
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42 Entrez.email = 'pedro_araujo97@hotmail.com'
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43 print('Working...')
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44 for phageID in self.data.index:
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45 with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=phageID) as handle:
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46 genomePhage = SeqIO.read(handle, "gb")
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47 protsPhage = {}
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48 for feat in genomePhage.features:
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49 if feat.type == 'CDS':
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50 try: protsPhage[feat.qualifiers['protein_id'][0]] = [feat.qualifiers['product'][0], feat.qualifiers['translation'][0]]
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51 except: pass
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52 self.phagesProteins[phageID] = protsPhage
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53
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54 for bact in self.all_bact:
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55 protsBac = {}
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56 with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=bact) as handle:
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57 genomeBac = SeqIO.read(handle, "gb")
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58 for feat in genomeBac.features:
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59 if feat.type == 'CDS':
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60 try: protsBac[feat.qualifiers['protein_id'][0]] = [feat.qualifiers['product'][0], feat.qualifiers['translation'][0]]
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61 except: pass
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62 self.bactProteins[bact] = protsBac
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63
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64 with open('files/phagesProteins.json', 'w') as f:
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65 json.dump(self.phagesProteins, f)
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66 self.__createFasta(self.phagesProteins, 'phagesProteins')
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67 with open('files/bactProteins.json', 'w') as f:
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68 json.dump(self.bactProteins, f)
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69 self.__createFasta(self.bactProteins, 'bactProteins')
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70 print('Done')
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71
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72 def addBacteriaFeatures(self):
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73 """
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74 For each unique bacteria present in the dataset, the DNA and protein sequences are saved in two variables.
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75 :return:
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76 """
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77 from Bio import Entrez
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78 from Bio import SeqIO
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79 import json
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80 import ast
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81 Entrez.email = 'pedro_araujo97@hotmail.com'
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82 print('Working...')
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83 for bact in self.all_bact:
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84 if bact not in self.bactProteins.keys():
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85 protsBac = {}
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86 try:
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87 with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=bact) as handle:
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88 genomeBac = SeqIO.read(handle, "gb")
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89 for feat in genomeBac.features:
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90 if feat.type == 'CDS':
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91 try: protsBac[feat.qualifiers['protein_id'][0]] = [feat.qualifiers['product'][0], feat.qualifiers['translation'][0]]
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92 except: pass
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93 if len(genomeBac.features) <= 5:
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94 with Entrez.efetch(db="nucleotide", rettype="gbwithparts", retmode="text", id=bact) as handle:
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95 genomeBac = handle.readlines()
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96 for i in range(len(genomeBac)):
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97 if ' CDS ' in genomeBac[i]:
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98 j = i
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99 protDone = False
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100 while j < len(genomeBac):
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101 if protDone:
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102 break
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103 if '/product=' in genomeBac[j]:
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104 product = genomeBac[j].strip()[10:]
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105 j += 1
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106 elif '_id=' in genomeBac[j]:
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107 protKey = genomeBac[j].strip()[13:-1]
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108 j += 1
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109 elif '/translation=' in genomeBac[j]:
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110 protSeq = genomeBac[j].strip()[14:]
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111 j += 1
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112 for k in range(j, len(genomeBac)):
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113 if genomeBac[k].islower():
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114 j = k
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115 protDone = True
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116 break
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117 else:
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118 protSeq += genomeBac[k].strip()
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119 else:
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120 j += 1
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121 protsBac[protKey] = [product, protSeq[:protSeq.find('"')]]
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122 self.bactProteins[bact] = protsBac
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123 except:
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124 print(bact + ' failed')
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125 with open('files/bactProteins.json', 'w') as f:
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126 json.dump(self.bactProteins, f)
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127 self.__createFasta(self.bactProteins, 'bactProteins')
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128 print('Done')
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129
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130 def add_individual_bacteria(self):
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131 """
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132 For each unique bacteria present in the dataset, the DNA and protein sequences are saved in two variables.
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133 :return:
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134 """
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135 from Bio import Entrez
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136 from Bio import SeqIO
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137 import json
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138 from pathlib import Path
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139 Entrez.email = 'pedro_araujo97@hotmail.com'
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140 print('Working...')
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141 for bact in self.all_bact:
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142 my_file = Path('files/bacteria/' + bact + ".json")
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143 if not my_file.is_file():
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144 protsBac = {}
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145 try:
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146 with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=bact) as handle:
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147 genomeBac = SeqIO.read(handle, "gb")
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148 for feat in genomeBac.features:
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149 if feat.type == 'CDS':
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150 try: protsBac[feat.qualifiers['protein_id'][0]] = [feat.qualifiers['product'][0], feat.qualifiers['translation'][0]]
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151 except: pass
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152 if len(genomeBac.features) <= 5:
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153 with Entrez.efetch(db="nucleotide", rettype="gbwithparts", retmode="text", id=bact) as handle:
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154 genomeBac = handle.readlines()
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155 for i in range(len(genomeBac)):
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156 if ' CDS ' in genomeBac[i]:
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157 j = i
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158 protDone = False
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159 while j < len(genomeBac):
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160 if protDone:
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161 break
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162 if '/product=' in genomeBac[j]:
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163 product = genomeBac[j].strip()[10:]
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164 j += 1
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165 elif '_id=' in genomeBac[j]:
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166 protKey = genomeBac[j].strip()[13:-1]
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167 j += 1
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168 elif '/translation=' in genomeBac[j]:
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169 protSeq = genomeBac[j].strip()[14:]
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170 j += 1
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171 for k in range(j, len(genomeBac)):
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172 if genomeBac[k].islower():
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173 j = k
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174 protDone = True
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175 break
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176 else:
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177 protSeq += genomeBac[k].strip()
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178 else:
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179 j += 1
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180 protsBac[protKey] = [product, protSeq[:protSeq.find('"')]]
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181 with open('files/bacteria/' + bact + '.json', 'w') as f:
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182 json.dump(protsBac, f)
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183 except:
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184 print(bact + ' failed')
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185 # with open('files/bactProteins.json', 'w') as f:
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186 # json.dump(self.bactProteins, f)
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187 # self.__createFasta(self.bactProteins, 'bactProteins')
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188 print('Done')
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189
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190 def importData(self):
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191 """
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192 Imports the previously saved DNA and protein sequences. This needs to be improved so the user can specify which data to import.
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193 :return:
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194 """
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195 import json
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196 with open('files/phagesProteins.json', encoding='utf-8') as F:
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197 self.phagesProteins = json.loads(F.read())
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198 # with open('files/bactProteins.json', encoding='utf-8') as F:
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199 # self.bactProteins = json.loads(F.read())
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200
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201 def addPhageProt(self):
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202 """
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203 For each unique phage present in the dataset, the DNA and protein sequences are saved in two variables.
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204 :return:
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205 """
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206 from Bio import Entrez
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207 from Bio import SeqIO
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208 import json
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209 Entrez.email = 'pedro_araujo97@hotmail.com'
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210 print('Working...')
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211
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212 for phageID in self.data.index:
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213 with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=phageID) as handle:
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214 genomePhage = SeqIO.read(handle, "gb")
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215 protsPhage = {}
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216 for feat in genomePhage.features:
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217 if feat.type == 'CDS':
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218 try: protsPhage[feat.qualifiers['protein_id'][0]] = [feat.qualifiers['product'][0], feat.qualifiers['translation'][0]]
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219 except: pass
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220 self.phagesProteins[phageID] = protsPhage
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221
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222 with open('files/phagesProteins.json', 'w') as f:
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223 json.dump(self.phagesProteins, f)
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224 self.__createFasta(self.phagesProteins, 'phagesProteins')
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225 return self.phagesProteins
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226
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227 def add_missing_phage(self):
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228 """
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229 For each unique phage present in the dataset, the DNA and protein sequences are saved in two variables.
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230 :return:
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231 """
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232 from Bio import Entrez
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233 from Bio import SeqIO
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234 import json
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235 Entrez.email = 'pedro_araujo97@hotmail.com'
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236 print('Working...')
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237
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238 for phageID in self.data.index:
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239 if phageID not in self.phagesProteins.keys():
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240 print(phageID)
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241 with Entrez.efetch(db="nucleotide", rettype="gb", retmode="text", id=phageID) as handle:
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242 genomePhage = SeqIO.read(handle, "gb")
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243 protsPhage = {}
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244 for feat in genomePhage.features:
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245 if feat.type == 'CDS':
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246 try: protsPhage[feat.qualifiers['protein_id'][0]] = [feat.qualifiers['product'][0], feat.qualifiers['translation'][0]]
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247 except: pass
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248 self.phagesProteins[phageID] = protsPhage
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249 with open('files/phagesProteins.json', 'w') as f:
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250 json.dump(self.phagesProteins, f)
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251 self.__createFasta(self.phagesProteins, 'phagesProteins')
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252 return self.phagesProteins
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253
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254 def __createFasta(self, var, name):
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255 with open('files/' + name + '.fasta', 'w') as F:
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256 for spec in var:
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257 try:
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258 for prot in var[spec]:
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259 F.write('>' + prot + '-' + spec + '\n' + var[spec][prot][1] + '\n')
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260 except:
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261 F.write('>' + spec + '\n' + var[spec] + '\n')
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262
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263
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264 if __name__ == '__main__':
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265 test = PhageBacteriaInformation('NCBI_Phage_Bacteria_Data.csv')
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266 test.add_individual_bacteria()
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267 test.addPhageProt()
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268 test.add_missing_phage()
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269 test.importData()
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