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1 from __future__ import division
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2 import sys
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3 import pandas as pd
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4 import itertools as it
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5 import scipy.stats as st
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6 import collections
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7 import lxml.etree as ET
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8 import shutil
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9 import pickle as pk
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10 import math
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11 import os
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12 import argparse
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13 from svglib.svglib import svg2rlg
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14 from reportlab.graphics import renderPDF
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15
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16 ########################## argparse ##########################################
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17
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18 def process_args(args):
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19 parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
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20 description = 'process some value\'s'+
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21 ' genes to create a comparison\'s map.')
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22 parser.add_argument('-rs', '--rules_selector',
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23 type = str,
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24 default = 'HMRcore',
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25 choices = ['HMRcore', 'Recon', 'Custom'],
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26 help = 'chose which type of dataset you want use')
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27 parser.add_argument('-cr', '--custom',
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28 type = str,
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29 help='your dataset if you want custom rules')
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30 parser.add_argument('-na', '--names',
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31 type = str,
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32 nargs = '+',
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33 help = 'input names')
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34 parser.add_argument('-n', '--none',
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35 type = str,
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36 default = 'true',
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37 choices = ['true', 'false'],
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38 help = 'compute Nan values')
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39 parser.add_argument('-pv' ,'--pValue',
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40 type = float,
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41 default = 0.05,
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42 help = 'P-Value threshold (default: %(default)s)')
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43 parser.add_argument('-fc', '--fChange',
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44 type = float,
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45 default = 1.5,
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46 help = 'Fold-Change threshold (default: %(default)s)')
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47 parser.add_argument('-td', '--tool_dir',
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48 type = str,
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49 required = True,
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50 help = 'your tool directory')
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51 parser.add_argument('-op', '--option',
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52 type = str,
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53 choices = ['datasets', 'dataset_class'],
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54 help='dataset or dataset and class')
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55 parser.add_argument('-ol', '--out_log',
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56 help = "Output log")
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57 parser.add_argument('-ids', '--input_datas',
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58 type = str,
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59 nargs = '+',
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60 help = 'input datasets')
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61 parser.add_argument('-id', '--input_data',
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62 type = str,
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63 help = 'input dataset')
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64 parser.add_argument('-ic', '--input_class',
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65 type = str,
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66 help = 'sample group specification')
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67 parser.add_argument('-cm', '--custom_map',
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68 type = str,
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69 help = 'custom map')
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70 parser.add_argument('-yn', '--yes_no',
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71 type = str,
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72 choices = ['yes', 'no'],
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73 help = 'if make or not custom map')
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74 parser.add_argument('-gs', '--generate_svg',
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75 type = str,
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76 default = 'true',
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77 choices = ['true', 'false'],
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78 help = 'generate svg map')
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79 parser.add_argument('-gp', '--generate_pdf',
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80 type = str,
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81 default = 'true',
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82 choices = ['true', 'false'],
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83 help = 'generate pdf map')
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84 parser.add_argument('-gr', '--generate_ras',
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85 type = str,
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86 default = 'true',
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87 choices = ['true', 'false'],
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88 help = 'generate reaction activity score')
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89 args = parser.parse_args()
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90 return args
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91
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92 ########################### warning ###########################################
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93
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94 def warning(s):
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95 args = process_args(sys.argv)
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96 with open(args.out_log, 'a') as log:
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97 log.write(s)
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98
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99 ############################ dataset input ####################################
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100
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101 def read_dataset(data, name):
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102 try:
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103 dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python')
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104 except pd.errors.EmptyDataError:
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105 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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106 if len(dataset.columns) < 2:
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107 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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108 return dataset
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109
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110 ############################ dataset name #####################################
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111
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112 def name_dataset(name_data, count):
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113 if str(name_data) == 'Dataset':
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114 return str(name_data) + '_' + str(count)
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115 else:
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116 return str(name_data)
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117
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118 ############################ load id e rules ##################################
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119
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120 def load_id_rules(reactions):
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121 ids, rules = [], []
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122 for key, value in reactions.items():
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123 ids.append(key)
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124 rules.append(value)
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125 return (ids, rules)
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126
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127 ############################ check_methods ####################################
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128
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129 def gene_type(l, name):
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130 if check_hgnc(l):
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131 return 'hugo_id'
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132 elif check_ensembl(l):
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133 return 'ensembl_gene_id'
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134 elif check_symbol(l):
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135 return 'symbol'
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136 elif check_entrez(l):
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137 return 'entrez_id'
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138 else:
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139 sys.exit('Execution aborted:\n' +
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140 'gene ID type in ' + name + ' not supported. Supported ID'+
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141 'types are: HUGO ID, Ensemble ID, HUGO symbol, Entrez ID\n')
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142
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143 def check_hgnc(l):
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144 if len(l) > 5:
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145 if (l.upper()).startswith('HGNC:'):
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146 return l[5:].isdigit()
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147 else:
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148 return False
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149 else:
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150 return False
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151
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152 def check_ensembl(l):
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153 if len(l) == 15:
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154 if (l.upper()).startswith('ENS'):
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155 return l[4:].isdigit()
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156 else:
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157 return False
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158 else:
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159 return False
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160
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161 def check_symbol(l):
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162 if len(l) > 0:
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163 if l[0].isalpha() and l[1:].isalnum():
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164 return True
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165 else:
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166 return False
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167 else:
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168 return False
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169
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170 def check_entrez(l):
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171 if len(l) > 0:
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172 return l.isdigit()
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173 else:
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174 return False
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175
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176 def check_bool(b):
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177 if b == 'true':
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178 return True
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179 elif b == 'false':
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180 return False
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181
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182 ############################ resolve_methods ##################################
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183
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184 def replace_gene_value(l, d):
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185 tmp = []
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186 err = []
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187 while l:
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188 if isinstance(l[0], list):
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189 tmp_rules, tmp_err = replace_gene_value(l[0], d)
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190 tmp.append(tmp_rules)
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191 err.extend(tmp_err)
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192 else:
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193 value = replace_gene(l[0], d)
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194 tmp.append(value)
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195 if value == None:
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196 err.append(l[0])
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197 l = l[1:]
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198 return (tmp, err)
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199
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200 def replace_gene(l, d):
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201 if l =='and' or l == 'or':
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202 return l
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203 else:
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204 value = d.get(l, None)
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205 if not(value == None or isinstance(value, (int, float))):
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206 sys.exit('Execution aborted: ' + value + ' value not valid\n')
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207 return value
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208
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209 def computes(val1, op, val2, cn):
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210 if val1 != None and val2 != None:
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211 if op == 'and':
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212 return min(val1, val2)
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213 else:
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214 return val1 + val2
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215 elif op == 'and':
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216 if cn is True:
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217 if val1 != None:
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218 return val1
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219 elif val2 != None:
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220 return val2
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221 else:
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222 return None
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223 else:
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224 return None
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225 else:
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226 if val1 != None:
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227 return val1
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228 elif val2 != None:
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229 return val2
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230 else:
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231 return None
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232
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233 def control(ris, l, cn):
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234 if len(l) == 1:
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235 if isinstance(l[0], (float, int)) or l[0] == None:
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236 return l[0]
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237 elif isinstance(l[0], list):
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238 return control(None, l[0], cn)
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239 else:
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240 return False
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241 elif len(l) > 2:
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242 return control_list(ris, l, cn)
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243 else:
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244 return False
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245
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246 def control_list(ris, l, cn):
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247 while l:
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248 if len(l) == 1:
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249 return False
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250 elif (isinstance(l[0], (float, int)) or
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251 l[0] == None) and l[1] in ['and', 'or']:
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252 if isinstance(l[2], (float, int)) or l[2] == None:
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253 ris = computes(l[0], l[1], l[2], cn)
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254 elif isinstance(l[2], list):
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255 tmp = control(None, l[2], cn)
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256 if tmp is False:
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257 return False
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258 else:
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259 ris = computes(l[0], l[1], tmp, cn)
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260 else:
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261 return False
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262 l = l[3:]
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263 elif l[0] in ['and', 'or']:
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264 if isinstance(l[1], (float, int)) or l[1] == None:
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265 ris = computes(ris, l[0], l[1], cn)
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266 elif isinstance(l[1], list):
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267 tmp = control(None,l[1], cn)
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268 if tmp is False:
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269 return False
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270 else:
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271 ris = computes(ris, l[0], tmp, cn)
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272 else:
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273 return False
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274 l = l[2:]
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275 elif isinstance(l[0], list) and l[1] in ['and', 'or']:
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276 if isinstance(l[2], (float, int)) or l[2] == None:
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277 tmp = control(None, l[0], cn)
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278 if tmp is False:
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279 return False
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280 else:
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281 ris = computes(tmp, l[1], l[2], cn)
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282 elif isinstance(l[2], list):
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283 tmp = control(None, l[0], cn)
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284 tmp2 = control(None, l[2], cn)
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285 if tmp is False or tmp2 is False:
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286 return False
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287 else:
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288 ris = computes(tmp, l[1], tmp2, cn)
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289 else:
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290 return False
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291 l = l[3:]
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292 else:
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293 return False
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294 return ris
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295
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296 ############################ map_methods ######################################
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297
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298 def fold_change(avg1, avg2):
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299 if avg1 == 0 and avg2 == 0:
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300 return 0
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301 elif avg1 == 0:
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302 return '-INF'
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303 elif avg2 == 0:
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304 return 'INF'
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305 else:
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306 return math.log(avg1 / avg2, 2)
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307
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308 def fix_style(l, col, width, dash):
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309 tmp = l.split(';')
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310 flag_col = False
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311 flag_width = False
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312 flag_dash = False
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313 for i in range(len(tmp)):
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314 if tmp[i].startswith('stroke:'):
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315 tmp[i] = 'stroke:' + col
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316 flag_col = True
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317 if tmp[i].startswith('stroke-width:'):
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318 tmp[i] = 'stroke-width:' + width
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319 flag_width = True
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320 if tmp[i].startswith('stroke-dasharray:'):
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321 tmp[i] = 'stroke-dasharray:' + dash
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322 flag_dash = True
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323 if not flag_col:
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324 tmp.append('stroke:' + col)
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325 if not flag_width:
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326 tmp.append('stroke-width:' + width)
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327 if not flag_dash:
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328 tmp.append('stroke-dasharray:' + dash)
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329 return ';'.join(tmp)
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330
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331 def fix_map(d, core_map, threshold_P_V, threshold_F_C, max_F_C):
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332 maxT = 12
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333 minT = 2
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334 grey = '#BEBEBE'
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335 blue = '#0000FF'
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336 red = '#E41A1C'
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337 for el in core_map.iter():
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338 el_id = str(el.get('id'))
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339 if el_id.startswith('R_'):
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340 tmp = d.get(el_id[2:])
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341 if tmp != None:
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342 p_val = tmp[0]
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343 f_c = tmp[1]
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344 if p_val < threshold_P_V:
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345 if not isinstance(f_c, str):
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346 if abs(f_c) < math.log(threshold_F_C, 2):
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347 col = grey
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348 width = str(minT)
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349 else:
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350 if f_c < 0:
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351 col = blue
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352 elif f_c > 0:
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353 col = red
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354 width = str(max((abs(f_c) * maxT) / max_F_C, minT))
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355 else:
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356 if f_c == '-INF':
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357 col = blue
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358 elif f_c == 'INF':
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359 col = red
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360 width = str(maxT)
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361 dash = 'none'
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362 else:
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363 dash = '5,5'
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364 col = grey
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365 width = str(minT)
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366 el.set('style', fix_style(el.get('style'), col, width, dash))
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367 return core_map
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368
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369 ############################ make recon #######################################
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370
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371 def check_and_doWord(l):
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372 tmp = []
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373 tmp_genes = []
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374 count = 0
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375 while l:
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376 if count >= 0:
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377 if l[0] == '(':
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378 count += 1
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379 tmp.append(l[0])
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380 l.pop(0)
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381 elif l[0] == ')':
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382 count -= 1
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383 tmp.append(l[0])
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384 l.pop(0)
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385 elif l[0] == ' ':
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386 l.pop(0)
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387 else:
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388 word = []
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389 while l:
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390 if l[0] in [' ', '(', ')']:
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391 break
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392 else:
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393 word.append(l[0])
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394 l.pop(0)
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395 word = ''.join(word)
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396 tmp.append(word)
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397 if not(word in ['or', 'and']):
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398 tmp_genes.append(word)
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399 else:
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400 return False
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401 if count == 0:
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402 return (tmp, tmp_genes)
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403 else:
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404 return False
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405
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406 def brackets_to_list(l):
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407 tmp = []
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408 while l:
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409 if l[0] == '(':
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410 l.pop(0)
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411 tmp.append(resolve_brackets(l))
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412 else:
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413 tmp.append(l[0])
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414 l.pop(0)
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415 return tmp
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416
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417 def resolve_brackets(l):
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418 tmp = []
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419 while l[0] != ')':
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420 if l[0] == '(':
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421 l.pop(0)
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422 tmp.append(resolve_brackets(l))
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423 else:
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424 tmp.append(l[0])
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425 l.pop(0)
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426 l.pop(0)
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427 return tmp
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428
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429 def priorityAND(l):
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430 tmp = []
|
|
|
431 flag = True
|
|
|
432 while l:
|
|
|
433 if len(l) == 1:
|
|
|
434 if isinstance(l[0], list):
|
|
|
435 tmp.append(priorityAND(l[0]))
|
|
|
436 else:
|
|
|
437 tmp.append(l[0])
|
|
|
438 l = l[1:]
|
|
|
439 elif l[0] == 'or':
|
|
|
440 tmp.append(l[0])
|
|
|
441 flag = False
|
|
|
442 l = l[1:]
|
|
|
443 elif l[1] == 'or':
|
|
|
444 if isinstance(l[0], list):
|
|
|
445 tmp.append(priorityAND(l[0]))
|
|
|
446 else:
|
|
|
447 tmp.append(l[0])
|
|
|
448 tmp.append(l[1])
|
|
|
449 flag = False
|
|
|
450 l = l[2:]
|
|
|
451 elif l[1] == 'and':
|
|
|
452 tmpAnd = []
|
|
|
453 if isinstance(l[0], list):
|
|
|
454 tmpAnd.append(priorityAND(l[0]))
|
|
|
455 else:
|
|
|
456 tmpAnd.append(l[0])
|
|
|
457 tmpAnd.append(l[1])
|
|
|
458 if isinstance(l[2], list):
|
|
|
459 tmpAnd.append(priorityAND(l[2]))
|
|
|
460 else:
|
|
|
461 tmpAnd.append(l[2])
|
|
|
462 l = l[3:]
|
|
|
463 while l:
|
|
|
464 if l[0] == 'and':
|
|
|
465 tmpAnd.append(l[0])
|
|
|
466 if isinstance(l[1], list):
|
|
|
467 tmpAnd.append(priorityAND(l[1]))
|
|
|
468 else:
|
|
|
469 tmpAnd.append(l[1])
|
|
|
470 l = l[2:]
|
|
|
471 elif l[0] == 'or':
|
|
|
472 flag = False
|
|
|
473 break
|
|
|
474 if flag == True: #when there are only AND in list
|
|
|
475 tmp.extend(tmpAnd)
|
|
|
476 elif flag == False:
|
|
|
477 tmp.append(tmpAnd)
|
|
|
478 return tmp
|
|
|
479
|
|
|
480 def checkRule(l):
|
|
|
481 if len(l) == 1:
|
|
|
482 if isinstance(l[0], list):
|
|
|
483 if checkRule(l[0]) is False:
|
|
|
484 return False
|
|
|
485 elif len(l) > 2:
|
|
|
486 if checkRule2(l) is False:
|
|
|
487 return False
|
|
|
488 else:
|
|
|
489 return False
|
|
|
490 return True
|
|
|
491
|
|
|
492 def checkRule2(l):
|
|
|
493 while l:
|
|
|
494 if len(l) == 1:
|
|
|
495 return False
|
|
|
496 elif isinstance(l[0], list) and l[1] in ['and', 'or']:
|
|
|
497 if checkRule(l[0]) is False:
|
|
|
498 return False
|
|
|
499 if isinstance(l[2], list):
|
|
|
500 if checkRule(l[2]) is False:
|
|
|
501 return False
|
|
|
502 l = l[3:]
|
|
|
503 elif l[1] in ['and', 'or']:
|
|
|
504 if isinstance(l[2], list):
|
|
|
505 if checkRule(l[2]) is False:
|
|
|
506 return False
|
|
|
507 l = l[3:]
|
|
|
508 elif l[0] in ['and', 'or']:
|
|
|
509 if isinstance(l[1], list):
|
|
|
510 if checkRule(l[1]) is False:
|
|
|
511 return False
|
|
|
512 l = l[2:]
|
|
|
513 else:
|
|
|
514 return False
|
|
|
515 return True
|
|
|
516
|
|
|
517 def do_rules(rules):
|
|
|
518 split_rules = []
|
|
|
519 err_rules = []
|
|
|
520 tmp_gene_in_rule = []
|
|
|
521 for i in range(len(rules)):
|
|
|
522 tmp = list(rules[i])
|
|
|
523 if tmp:
|
|
|
524 tmp, tmp_genes = check_and_doWord(tmp)
|
|
|
525 tmp_gene_in_rule.extend(tmp_genes)
|
|
|
526 if tmp is False:
|
|
|
527 split_rules.append([])
|
|
|
528 err_rules.append(rules[i])
|
|
|
529 else:
|
|
|
530 tmp = brackets_to_list(tmp)
|
|
|
531 if checkRule(tmp):
|
|
|
532 split_rules.append(priorityAND(tmp))
|
|
|
533 else:
|
|
|
534 split_rules.append([])
|
|
|
535 err_rules.append(rules[i])
|
|
|
536 else:
|
|
|
537 split_rules.append([])
|
|
|
538 if err_rules:
|
|
|
539 warning('Warning: wrong format rule in ' + str(err_rules) + '\n')
|
|
|
540 return (split_rules, list(set(tmp_gene_in_rule)))
|
|
|
541
|
|
|
542 def make_recon(data):
|
|
|
543 try:
|
|
|
544 import cobra as cb
|
|
|
545 import warnings
|
|
|
546 with warnings.catch_warnings():
|
|
|
547 warnings.simplefilter('ignore')
|
|
|
548 recon = cb.io.read_sbml_model(data)
|
|
|
549 react = recon.reactions
|
|
|
550 rules = [react[i].gene_reaction_rule for i in range(len(react))]
|
|
|
551 ids = [react[i].id for i in range(len(react))]
|
|
|
552 except cb.io.sbml3.CobraSBMLError:
|
|
|
553 try:
|
|
|
554 data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('')
|
|
|
555 if len(data.columns) < 2:
|
|
|
556 sys.exit('Execution aborted: wrong format of '+
|
|
|
557 'custom datarules\n')
|
|
|
558 if not len(data.columns) == 2:
|
|
|
559 warning('Warning: more than 2 columns in custom datarules.\n' +
|
|
|
560 'Extra columns have been disregarded\n')
|
|
|
561 ids = list(data.iloc[:, 0])
|
|
|
562 rules = list(data.iloc[:, 1])
|
|
|
563 except pd.errors.EmptyDataError:
|
|
|
564 sys.exit('Execution aborted: wrong format of custom datarules\n')
|
|
|
565 except pd.errors.ParserError:
|
|
|
566 sys.exit('Execution aborted: wrong format of custom datarules\n')
|
|
|
567 split_rules, tmp_genes = do_rules(rules)
|
|
|
568 gene_in_rule = {}
|
|
|
569 for i in tmp_genes:
|
|
|
570 gene_in_rule[i] = 'ok'
|
|
|
571 return (ids, split_rules, gene_in_rule)
|
|
|
572
|
|
|
573 ############################ gene #############################################
|
|
|
574
|
|
|
575 def data_gene(gene, type_gene, name, gene_custom):
|
|
|
576 args = process_args(sys.argv)
|
|
|
577 for i in range(len(gene)):
|
|
|
578 tmp = gene.iloc[i, 0]
|
|
|
579 if tmp.startswith(' ') or tmp.endswith(' '):
|
|
|
580 gene.iloc[i, 0] = (tmp.lstrip()).rstrip()
|
|
|
581 gene_dup = [item for item, count in
|
|
|
582 collections.Counter(gene[gene.columns[0]]).items() if count > 1]
|
|
|
583 pat_dup = [item for item, count in
|
|
|
584 collections.Counter(list(gene.columns)).items() if count > 1]
|
|
|
585 if gene_dup:
|
|
|
586 if gene_custom == None:
|
|
|
587 if args.rules_selector == 'HMRcore':
|
|
|
588 gene_in_rule = pk.load(open(args.tool_dir +
|
|
|
589 '/local/HMRcore_genes.p', 'rb'))
|
|
|
590 elif args.rules_selector == 'Recon':
|
|
|
591 gene_in_rule = pk.load(open(args.tool_dir +
|
|
|
592 '/local/Recon_genes.p', 'rb'))
|
|
|
593 gene_in_rule = gene_in_rule.get(type_gene)
|
|
|
594 else:
|
|
|
595 gene_in_rule = gene_custom
|
|
|
596 tmp = []
|
|
|
597 for i in gene_dup:
|
|
|
598 if gene_in_rule.get(i) == 'ok':
|
|
|
599 tmp.append(i)
|
|
|
600 if tmp:
|
|
|
601 sys.exit('Execution aborted because gene ID '
|
|
|
602 +str(tmp)+' in '+name+' is duplicated\n')
|
|
|
603 if pat_dup:
|
|
|
604 warning('Warning: duplicated label\n' + str(pat_dup) + 'in ' + name +
|
|
|
605 '\n')
|
|
|
606 return (gene.set_index(gene.columns[0])).to_dict()
|
|
|
607
|
|
|
608 ############################ resolve ##########################################
|
|
|
609
|
|
|
610 def resolve(genes, rules, ids, resolve_none, name):
|
|
|
611 resolve_rules = {}
|
|
|
612 not_found = []
|
|
|
613 flag = False
|
|
|
614 for key, value in genes.items():
|
|
|
615 tmp_resolve = []
|
|
|
616 for i in range(len(rules)):
|
|
|
617 tmp = rules[i]
|
|
|
618 if tmp:
|
|
|
619 tmp, err = replace_gene_value(tmp, value)
|
|
|
620 if err:
|
|
|
621 not_found.extend(err)
|
|
|
622 ris = control(None, tmp, resolve_none)
|
|
|
623 if ris is False or ris == None:
|
|
|
624 tmp_resolve.append(None)
|
|
|
625 else:
|
|
|
626 tmp_resolve.append(ris)
|
|
|
627 flag = True
|
|
|
628 else:
|
|
|
629 tmp_resolve.append(None)
|
|
|
630 resolve_rules[key] = tmp_resolve
|
|
|
631 if flag is False:
|
|
|
632 warning('Warning: no computable score (due to missing gene values)' +
|
|
|
633 'for class ' + name + ', the class has been disregarded\n')
|
|
|
634 return (None, None)
|
|
|
635 return (resolve_rules, list(set(not_found)))
|
|
|
636
|
|
|
637 ############################ split class ######################################
|
|
|
638
|
|
|
639 def split_class(classes, resolve_rules):
|
|
|
640 class_pat = {}
|
|
|
641 for i in range(len(classes)):
|
|
|
642 classe = classes.iloc[i, 1]
|
|
|
643 if not pd.isnull(classe):
|
|
|
644 l = []
|
|
|
645 for j in range(i, len(classes)):
|
|
|
646 if classes.iloc[j, 1] == classe:
|
|
|
647 pat_id = classes.iloc[j, 0]
|
|
|
648 tmp = resolve_rules.get(pat_id, None)
|
|
|
649 if tmp != None:
|
|
|
650 l.append(tmp)
|
|
|
651 classes.iloc[j, 1] = None
|
|
|
652 if l:
|
|
|
653 class_pat[classe] = list(map(list, zip(*l)))
|
|
|
654 else:
|
|
|
655 warning('Warning: no sample found in class ' + classe +
|
|
|
656 ', the class has been disregarded\n')
|
|
|
657 return class_pat
|
|
|
658
|
|
|
659 ############################ create_ras #######################################
|
|
|
660
|
|
|
661 def create_ras (resolve_rules, dataset_name):
|
|
|
662
|
|
|
663 if resolve_rules == None:
|
|
|
664 warning("Couldn't generate RAS for current dataset: " + dataset_name)
|
|
|
665
|
|
|
666 for geni in resolve_rules.values():
|
|
|
667 for i, valori in enumerate(geni):
|
|
|
668 if valori == None:
|
|
|
669 geni[i] = 'None'
|
|
|
670
|
|
|
671 output_ras = pd.DataFrame.from_dict(resolve_rules)
|
|
|
672 output_to_csv = pd.DataFrame.to_csv(output_ras, sep = '\t', index = False)
|
|
|
673
|
|
|
674 text_file = open("ras/Reaction_Activity_Score_Of_" + dataset_name + ".tsv", "w")
|
|
|
675 text_file.write(output_to_csv)
|
|
|
676 text_file.close()
|
|
|
677
|
|
|
678 ############################ map ##############################################
|
|
|
679
|
|
|
680 def maps(core_map, class_pat, ids, threshold_P_V, threshold_F_C, create_svg, create_pdf):
|
|
|
681 args = process_args(sys.argv)
|
|
|
682 if (not class_pat) or (len(class_pat.keys()) < 2):
|
|
|
683 sys.exit('Execution aborted: classes provided for comparisons are ' +
|
|
|
684 'less than two\n')
|
|
|
685 for i, j in it.combinations(class_pat.keys(), 2):
|
|
|
686 tmp = {}
|
|
|
687 count = 0
|
|
|
688 max_F_C = 0
|
|
|
689 for l1, l2 in zip(class_pat.get(i), class_pat.get(j)):
|
|
|
690 try:
|
|
|
691 stat_D, p_value = st.ks_2samp(l1, l2)
|
|
|
692 avg = fold_change(sum(l1) / len(l1), sum(l2) / len(l2))
|
|
|
693 if not isinstance(avg, str):
|
|
|
694 if max_F_C < abs(avg):
|
|
|
695 max_F_C = abs(avg)
|
|
|
696 tmp[ids[count]] = [float(p_value), avg]
|
|
|
697 count += 1
|
|
|
698 except (TypeError, ZeroDivisionError):
|
|
|
699 count += 1
|
|
|
700 tab = 'result/' + i + '_vs_' + j + ' (Tabular Result).tsv'
|
|
|
701 tmp_csv = pd.DataFrame.from_dict(tmp, orient = "index")
|
|
|
702 tmp_csv = tmp_csv.reset_index()
|
|
|
703 header = ['ids', 'P_Value', 'Average']
|
|
|
704 tmp_csv.to_csv(tab, sep = '\t', index = False, header = header)
|
|
|
705
|
|
|
706 if create_svg or create_pdf:
|
|
|
707 if args.rules_selector == 'HMRcore' or (args.rules_selector == 'Custom'
|
|
|
708 and args.yes_no == 'yes'):
|
|
|
709 fix_map(tmp, core_map, threshold_P_V, threshold_F_C, max_F_C)
|
|
|
710 file_svg = 'result/' + i + '_vs_' + j + ' (SVG Map).svg'
|
|
|
711 with open(file_svg, 'wb') as new_map:
|
|
|
712 new_map.write(ET.tostring(core_map))
|
|
|
713
|
|
|
714
|
|
|
715 if create_pdf:
|
|
|
716 file_pdf = 'result/' + i + '_vs_' + j + ' (PDF Map).pdf'
|
|
|
717 renderPDF.drawToFile(svg2rlg(file_svg), file_pdf)
|
|
|
718
|
|
|
719 if not create_svg:
|
|
|
720 #Ho utilizzato il file svg per generare il pdf,
|
|
|
721 #ma l'utente non ne ha richiesto il ritorno, quindi
|
|
|
722 #lo elimino
|
|
|
723 os.remove('result/' + i + '_vs_' + j + ' (SVG Map).svg')
|
|
|
724
|
|
|
725 return None
|
|
|
726
|
|
|
727 ############################ MAIN #############################################
|
|
|
728
|
|
|
729 def main():
|
|
|
730 args = process_args(sys.argv)
|
|
|
731
|
|
|
732 create_svg = check_bool(args.generate_svg)
|
|
|
733 create_pdf = check_bool(args.generate_pdf)
|
|
|
734 generate_ras = check_bool(args.generate_ras)
|
|
|
735
|
|
|
736 os.makedirs('result')
|
|
|
737
|
|
|
738 if generate_ras:
|
|
|
739 os.makedirs('ras')
|
|
|
740
|
|
|
741 if args.rules_selector == 'HMRcore':
|
|
|
742 recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb'))
|
|
|
743 elif args.rules_selector == 'Recon':
|
|
|
744 recon = pk.load(open(args.tool_dir + '/local/Recon_rules.p', 'rb'))
|
|
|
745 elif args.rules_selector == 'Custom':
|
|
|
746 ids, rules, gene_in_rule = make_recon(args.custom)
|
|
|
747
|
|
|
748 resolve_none = check_bool(args.none)
|
|
|
749
|
|
|
750 class_pat = {}
|
|
|
751
|
|
|
752 if args.option == 'datasets':
|
|
|
753 num = 1
|
|
|
754 for i, j in zip(args.input_datas, args.names):
|
|
|
755
|
|
|
756 name = name_dataset(j, num)
|
|
|
757 dataset = read_dataset(i, name)
|
|
|
758
|
|
|
759 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
|
|
|
760
|
|
|
761 type_gene = gene_type(dataset.iloc[0, 0], name)
|
|
|
762
|
|
|
763 if args.rules_selector != 'Custom':
|
|
|
764 genes = data_gene(dataset, type_gene, name, None)
|
|
|
765 ids, rules = load_id_rules(recon.get(type_gene))
|
|
|
766 elif args.rules_selector == 'Custom':
|
|
|
767 genes = data_gene(dataset, type_gene, name, gene_in_rule)
|
|
|
768
|
|
|
769 resolve_rules, err = resolve(genes, rules, ids, resolve_none, name)
|
|
|
770
|
|
|
771 if generate_ras:
|
|
|
772 create_ras(resolve_rules, name)
|
|
|
773
|
|
|
774
|
|
|
775 if err != None and err:
|
|
|
776 warning('Warning: gene\n' + str(err) + '\nnot found in class '
|
|
|
777 + name + ', the expression level for this gene ' +
|
|
|
778 'will be considered NaN\n')
|
|
|
779 if resolve_rules != None:
|
|
|
780 class_pat[name] = list(map(list, zip(*resolve_rules.values())))
|
|
|
781 num += 1
|
|
|
782 elif args.option == 'dataset_class':
|
|
|
783 name = 'RNAseq'
|
|
|
784 dataset = read_dataset(args.input_data, name)
|
|
|
785 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
|
|
|
786 type_gene = gene_type(dataset.iloc[0, 0], name)
|
|
|
787 classes = read_dataset(args.input_class, 'class')
|
|
|
788 if not len(classes.columns) == 2:
|
|
|
789 warning('Warning: more than 2 columns in class file. Extra' +
|
|
|
790 'columns have been disregarded\n')
|
|
|
791 classes = classes.astype(str)
|
|
|
792 if args.rules_selector != 'Custom':
|
|
|
793 genes = data_gene(dataset, type_gene, name, None)
|
|
|
794 ids, rules = load_id_rules(recon.get(type_gene))
|
|
|
795 elif args.rules_selector == 'Custom':
|
|
|
796 genes = data_gene(dataset, type_gene, name, gene_in_rule)
|
|
|
797 resolve_rules, err = resolve(genes, rules, ids, resolve_none, name)
|
|
|
798 if err != None and err:
|
|
|
799 warning('Warning: gene\n'+str(err)+'\nnot found in class '
|
|
|
800 + name + ', the expression level for this gene ' +
|
|
|
801 'will be considered NaN\n')
|
|
|
802 if resolve_rules != None:
|
|
|
803 class_pat = split_class(classes, resolve_rules)
|
|
|
804
|
|
|
805 if args.rules_selector == 'Custom':
|
|
|
806 if args.yes_no == 'yes':
|
|
|
807 try:
|
|
|
808 core_map = ET.parse(args.custom_map)
|
|
|
809 except (ET.XMLSyntaxError, ET.XMLSchemaParseError):
|
|
|
810 sys.exit('Execution aborted: custom map in wrong format')
|
|
|
811 elif args.yes_no == 'no':
|
|
|
812 core_map = ET.parse(args.tool_dir + '/local/HMRcoreMap.svg')
|
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813 else:
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814 core_map = ET.parse(args.tool_dir+'/local/HMRcoreMap.svg')
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815
|
|
|
816 maps(core_map, class_pat, ids, args.pValue, args.fChange, create_svg, create_pdf)
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817
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|
|
818 print('Execution succeded')
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|
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819
|
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820 return None
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821
|
|
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822 ###############################################################################
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823
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824 if __name__ == "__main__":
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825 main()
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