annotate Marea/ras_generator.py @ 68:aa09186cbc9f draft

Uploaded
author bimib
date Thu, 23 Apr 2020 17:03:48 -0400
parents 3af9d394367c
children 3b0e71e28c0b
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bimib
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1 from __future__ import division
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bimib
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2 import sys
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bimib
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3 import pandas as pd
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bimib
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4 import collections
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bimib
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5 import pickle as pk
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bimib
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6 import math
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bimib
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7 import argparse
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bimib
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8
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bimib
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9 ########################## argparse ##########################################
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10
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11 def process_args(args):
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12 parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
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13 description = 'process some value\'s'+
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14 ' genes to create a comparison\'s map.')
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15 parser.add_argument('-rs', '--rules_selector',
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16 type = str,
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17 default = 'HMRcore',
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18 choices = ['HMRcore', 'Recon', 'Custom'],
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19 help = 'chose which type of dataset you want use')
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20 parser.add_argument('-cr', '--custom',
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21 type = str,
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22 help='your dataset if you want custom rules')
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23 parser.add_argument('-n', '--none',
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24 type = str,
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25 default = 'true',
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26 choices = ['true', 'false'],
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27 help = 'compute Nan values')
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28 parser.add_argument('-td', '--tool_dir',
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29 type = str,
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30 required = True,
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31 help = 'your tool directory')
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32 parser.add_argument('-ol', '--out_log',
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33 help = "Output log")
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34 parser.add_argument('-id', '--input',
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35 type = str,
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36 help = 'input dataset')
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37 parser.add_argument('-ra', '--ras_output',
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38 type = str,
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39 required = True,
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40 help = 'ras output')
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41
46
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42 args = parser.parse_args()
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43 return args
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44
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bimib
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45 ########################### warning ###########################################
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46
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47 def warning(s):
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48 args = process_args(sys.argv)
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49 with open(args.out_log, 'a') as log:
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50 log.write(s)
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51
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52 ############################ dataset input ####################################
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53
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54 def read_dataset(data, name):
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55 try:
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56 dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python')
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57 except pd.errors.EmptyDataError:
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58 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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59 if len(dataset.columns) < 2:
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60 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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61 return dataset
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62
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63 ############################ dataset name #####################################
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64
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65 def name_dataset(name_data, count):
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66 if str(name_data) == 'Dataset':
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67 return str(name_data) + '_' + str(count)
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68 else:
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69 return str(name_data)
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70
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71 ############################ load id e rules ##################################
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72
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73 def load_id_rules(reactions):
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74 ids, rules = [], []
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75 for key, value in reactions.items():
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76 ids.append(key)
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77 rules.append(value)
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78 return (ids, rules)
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79
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80 ############################ check_methods ####################################
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81
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82 def gene_type(l, name):
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83 if check_hgnc(l):
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84 return 'hugo_id'
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85 elif check_ensembl(l):
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86 return 'ensembl_gene_id'
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87 elif check_symbol(l):
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88 return 'symbol'
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89 elif check_entrez(l):
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90 return 'entrez_id'
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91 else:
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92 sys.exit('Execution aborted:\n' +
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93 'gene ID type in ' + name + ' not supported. Supported ID'+
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94 'types are: HUGO ID, Ensemble ID, HUGO symbol, Entrez ID\n')
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95
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96 def check_hgnc(l):
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97 if len(l) > 5:
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98 if (l.upper()).startswith('HGNC:'):
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99 return l[5:].isdigit()
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100 else:
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101 return False
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102 else:
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103 return False
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104
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105 def check_ensembl(l):
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106 if len(l) == 15:
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107 if (l.upper()).startswith('ENS'):
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108 return l[4:].isdigit()
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109 else:
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110 return False
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111 else:
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112 return False
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113
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114 def check_symbol(l):
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115 if len(l) > 0:
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116 if l[0].isalpha() and l[1:].isalnum():
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117 return True
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118 else:
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119 return False
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120 else:
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121 return False
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122
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123 def check_entrez(l):
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124 if len(l) > 0:
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125 return l.isdigit()
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126 else:
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127 return False
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128
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129 def check_bool(b):
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130 if b == 'true':
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131 return True
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132 elif b == 'false':
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133 return False
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134
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135 ############################ resolve_methods ##################################
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136
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137 def replace_gene_value(l, d):
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138 tmp = []
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139 err = []
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140 while l:
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141 if isinstance(l[0], list):
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142 tmp_rules, tmp_err = replace_gene_value(l[0], d)
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143 tmp.append(tmp_rules)
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144 err.extend(tmp_err)
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145 else:
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146 value = replace_gene(l[0], d)
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147 tmp.append(value)
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148 if value == None:
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149 err.append(l[0])
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150 l = l[1:]
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151 return (tmp, err)
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152
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153
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154 def replace_gene(l, d):
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155 if l =='and' or l == 'or':
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156 return l
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157 else:
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158 value = d.get(l, None)
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159 if not(value == None or isinstance(value, (int, float))):
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160 sys.exit('Execution aborted: ' + value + ' value not valid\n')
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161 return value
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162
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163 def computes(val1, op, val2, cn):
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164 if val1 != None and val2 != None:
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165 if op == 'and':
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166 return min(val1, val2)
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167 else:
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168 return val1 + val2
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169 elif op == 'and':
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170 if cn is True:
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171 if val1 != None:
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172 return val1
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173 elif val2 != None:
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174 return val2
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175 else:
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176 return None
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177 else:
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178 return None
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179 else:
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bimib
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180 if val1 != None:
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181 return val1
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182 elif val2 != None:
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183 return val2
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184 else:
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185 return None
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186
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187 def control(ris, l, cn):
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188 if len(l) == 1:
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189 if isinstance(l[0], (float, int)) or l[0] == None:
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190 return l[0]
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191 elif isinstance(l[0], list):
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192 return control(None, l[0], cn)
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193 else:
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194 return False
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195 elif len(l) > 2:
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196 return control_list(ris, l, cn)
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197 else:
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198 return False
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199
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200 def control_list(ris, l, cn):
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201 while l:
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202 if len(l) == 1:
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203 return False
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204 elif (isinstance(l[0], (float, int)) or
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205 l[0] == None) and l[1] in ['and', 'or']:
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206 if isinstance(l[2], (float, int)) or l[2] == None:
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207 ris = computes(l[0], l[1], l[2], cn)
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208 elif isinstance(l[2], list):
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209 tmp = control(None, l[2], cn)
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210 if tmp is False:
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211 return False
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212 else:
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213 ris = computes(l[0], l[1], tmp, cn)
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diff changeset
214 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
215 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
216 l = l[3:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
217 elif l[0] in ['and', 'or']:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
218 if isinstance(l[1], (float, int)) or l[1] == None:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
219 ris = computes(ris, l[0], l[1], cn)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
220 elif isinstance(l[1], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
221 tmp = control(None,l[1], cn)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
222 if tmp is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
223 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
224 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
225 ris = computes(ris, l[0], tmp, cn)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
226 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
227 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
228 l = l[2:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
229 elif isinstance(l[0], list) and l[1] in ['and', 'or']:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
230 if isinstance(l[2], (float, int)) or l[2] == None:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
231 tmp = control(None, l[0], cn)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
232 if tmp is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
233 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
234 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
235 ris = computes(tmp, l[1], l[2], cn)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
236 elif isinstance(l[2], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
237 tmp = control(None, l[0], cn)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
238 tmp2 = control(None, l[2], cn)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
239 if tmp is False or tmp2 is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
240 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
241 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
242 ris = computes(tmp, l[1], tmp2, cn)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
243 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
244 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
245 l = l[3:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
246 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
247 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
248 return ris
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
249
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
250 ############################ make recon #######################################
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
251
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
252 def check_and_doWord(l):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
253 tmp = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
254 tmp_genes = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
255 count = 0
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
256 while l:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
257 if count >= 0:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
258 if l[0] == '(':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
259 count += 1
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
260 tmp.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
261 l.pop(0)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
262 elif l[0] == ')':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
263 count -= 1
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
264 tmp.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
265 l.pop(0)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
266 elif l[0] == ' ':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
267 l.pop(0)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
268 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
269 word = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
270 while l:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
271 if l[0] in [' ', '(', ')']:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
272 break
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
273 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
274 word.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
275 l.pop(0)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
276 word = ''.join(word)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
277 tmp.append(word)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
278 if not(word in ['or', 'and']):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
279 tmp_genes.append(word)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
280 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
281 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
282 if count == 0:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
283 return (tmp, tmp_genes)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
284 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
285 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
286
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
287 def brackets_to_list(l):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
288 tmp = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
289 while l:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
290 if l[0] == '(':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
291 l.pop(0)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
292 tmp.append(resolve_brackets(l))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
293 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
294 tmp.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
295 l.pop(0)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
296 return tmp
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
297
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
298 def resolve_brackets(l):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
299 tmp = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
300 while l[0] != ')':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
301 if l[0] == '(':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
302 l.pop(0)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
303 tmp.append(resolve_brackets(l))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
304 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
305 tmp.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
306 l.pop(0)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
307 l.pop(0)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
308 return tmp
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
309
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
310 def priorityAND(l):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
311 tmp = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
312 flag = True
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
313 while l:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
314 if len(l) == 1:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
315 if isinstance(l[0], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
316 tmp.append(priorityAND(l[0]))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
317 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
318 tmp.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
319 l = l[1:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
320 elif l[0] == 'or':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
321 tmp.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
322 flag = False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
323 l = l[1:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
324 elif l[1] == 'or':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
325 if isinstance(l[0], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
326 tmp.append(priorityAND(l[0]))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
327 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
328 tmp.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
329 tmp.append(l[1])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
330 flag = False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
331 l = l[2:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
332 elif l[1] == 'and':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
333 tmpAnd = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
334 if isinstance(l[0], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
335 tmpAnd.append(priorityAND(l[0]))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
336 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
337 tmpAnd.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
338 tmpAnd.append(l[1])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
339 if isinstance(l[2], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
340 tmpAnd.append(priorityAND(l[2]))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
341 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
342 tmpAnd.append(l[2])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
343 l = l[3:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
344 while l:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
345 if l[0] == 'and':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
346 tmpAnd.append(l[0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
347 if isinstance(l[1], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
348 tmpAnd.append(priorityAND(l[1]))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
349 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
350 tmpAnd.append(l[1])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
351 l = l[2:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
352 elif l[0] == 'or':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
353 flag = False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
354 break
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
355 if flag == True: #when there are only AND in list
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
356 tmp.extend(tmpAnd)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
357 elif flag == False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
358 tmp.append(tmpAnd)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
359 return tmp
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
360
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
361 def checkRule(l):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
362 if len(l) == 1:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
363 if isinstance(l[0], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
364 if checkRule(l[0]) is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
365 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
366 elif len(l) > 2:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
367 if checkRule2(l) is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
368 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
369 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
370 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
371 return True
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
372
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
373 def checkRule2(l):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
374 while l:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
375 if len(l) == 1:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
376 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
377 elif isinstance(l[0], list) and l[1] in ['and', 'or']:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
378 if checkRule(l[0]) is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
379 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
380 if isinstance(l[2], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
381 if checkRule(l[2]) is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
382 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
383 l = l[3:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
384 elif l[1] in ['and', 'or']:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
385 if isinstance(l[2], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
386 if checkRule(l[2]) is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
387 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
388 l = l[3:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
389 elif l[0] in ['and', 'or']:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
390 if isinstance(l[1], list):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
391 if checkRule(l[1]) is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
392 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
393 l = l[2:]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
394 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
395 return False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
396 return True
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
397
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
398 def do_rules(rules):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
399 split_rules = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
400 err_rules = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
401 tmp_gene_in_rule = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
402 for i in range(len(rules)):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
403 tmp = list(rules[i])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
404 if tmp:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
405 tmp, tmp_genes = check_and_doWord(tmp)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
406 tmp_gene_in_rule.extend(tmp_genes)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
407 if tmp is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
408 split_rules.append([])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
409 err_rules.append(rules[i])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
410 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
411 tmp = brackets_to_list(tmp)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
412 if checkRule(tmp):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
413 split_rules.append(priorityAND(tmp))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
414 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
415 split_rules.append([])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
416 err_rules.append(rules[i])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
417 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
418 split_rules.append([])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
419 if err_rules:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
420 warning('Warning: wrong format rule in ' + str(err_rules) + '\n')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
421 return (split_rules, list(set(tmp_gene_in_rule)))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
422
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
423 def make_recon(data):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
424 try:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
425 import cobra as cb
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
426 import warnings
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
427 with warnings.catch_warnings():
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
428 warnings.simplefilter('ignore')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
429 recon = cb.io.read_sbml_model(data)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
430 react = recon.reactions
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
431 rules = [react[i].gene_reaction_rule for i in range(len(react))]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
432 ids = [react[i].id for i in range(len(react))]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
433 except cb.io.sbml3.CobraSBMLError:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
434 try:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
435 data = (pd.read_csv(data, sep = '\t', dtype = str, engine='python')).fillna('')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
436 if len(data.columns) < 2:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
437 sys.exit('Execution aborted: wrong format of '+
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
438 'custom datarules\n')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
439 if not len(data.columns) == 2:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
440 warning('Warning: more than 2 columns in custom datarules.\n' +
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
441 'Extra columns have been disregarded\n')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
442 ids = list(data.iloc[:, 0])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
443 rules = list(data.iloc[:, 1])
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
444 except pd.errors.EmptyDataError:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
445 sys.exit('Execution aborted: wrong format of custom datarules\n')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
446 except pd.errors.ParserError:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
447 sys.exit('Execution aborted: wrong format of custom datarules\n')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
448 split_rules, tmp_genes = do_rules(rules)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
449 gene_in_rule = {}
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
450 for i in tmp_genes:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
451 gene_in_rule[i] = 'ok'
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
452 return (ids, split_rules, gene_in_rule)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
453
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
454 ############################ gene #############################################
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
455
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
456 def data_gene(gene, type_gene, name, gene_custom):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
457 args = process_args(sys.argv)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
458 for i in range(len(gene)):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
459 tmp = gene.iloc[i, 0]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
460 if tmp.startswith(' ') or tmp.endswith(' '):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
461 gene.iloc[i, 0] = (tmp.lstrip()).rstrip()
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
462 gene_dup = [item for item, count in
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
463 collections.Counter(gene[gene.columns[0]]).items() if count > 1]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
464 pat_dup = [item for item, count in
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
465 collections.Counter(list(gene.columns)).items() if count > 1]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
466
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
467 if gene_dup:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
468 if gene_custom == None:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
469 if args.rules_selector == 'HMRcore':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
470 gene_in_rule = pk.load(open(args.tool_dir +
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
471 '/local/HMRcore_genes.p', 'rb'))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
472 elif args.rules_selector == 'Recon':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
473 gene_in_rule = pk.load(open(args.tool_dir +
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
474 '/local/Recon_genes.p', 'rb'))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
475 gene_in_rule = gene_in_rule.get(type_gene)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
476 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
477 gene_in_rule = gene_custom
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
478 tmp = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
479 for i in gene_dup:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
480 if gene_in_rule.get(i) == 'ok':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
481 tmp.append(i)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
482 if tmp:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
483 sys.exit('Execution aborted because gene ID '
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
484 +str(tmp)+' in '+name+' is duplicated\n')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
485 if pat_dup:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
486 warning('Warning: duplicated label\n' + str(pat_dup) + 'in ' + name +
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
487 '\n')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
488
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
489 return (gene.set_index(gene.columns[0])).to_dict()
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
490
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
491 ############################ resolve ##########################################
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
492
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
493 def resolve(genes, rules, ids, resolve_none, name):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
494 resolve_rules = {}
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
495 not_found = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
496 flag = False
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
497 for key, value in genes.items():
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
498 tmp_resolve = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
499 for i in range(len(rules)):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
500 tmp = rules[i]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
501 if tmp:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
502 tmp, err = replace_gene_value(tmp, value)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
503 if err:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
504 not_found.extend(err)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
505 ris = control(None, tmp, resolve_none)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
506 if ris is False or ris == None:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
507 tmp_resolve.append(None)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
508 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
509 tmp_resolve.append(ris)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
510 flag = True
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
511 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
512 tmp_resolve.append(None)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
513 resolve_rules[key] = tmp_resolve
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
514 if flag is False:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
515 warning('Warning: no computable score (due to missing gene values)' +
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
516 'for class ' + name + ', the class has been disregarded\n')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
517 return (None, None)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
518 return (resolve_rules, list(set(not_found)))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
519
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
520 ############################ split class ######################################
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
521
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
522 def split_class(classes, resolve_rules):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
523 class_pat = {}
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
524 for i in range(len(classes)):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
525 classe = classes.iloc[i, 1]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
526 if not pd.isnull(classe):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
527 l = []
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
528 for j in range(i, len(classes)):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
529 if classes.iloc[j, 1] == classe:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
530 pat_id = classes.iloc[j, 0]
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
531 if tmp != None:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
532 l.append(tmp)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
533 classes.iloc[j, 1] = None
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
534 if l:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
535 class_pat[classe] = list(map(list, zip(*l)))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
536 else:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
537 warning('Warning: no sample found in class ' + classe +
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
538 ', the class has been disregarded\n')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
539 return class_pat
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
540
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
541 ############################ create_ras #######################################
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
542
47
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
543 def create_ras (resolve_rules, dataset_name, rules, ids, file):
46
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
544
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
545 if resolve_rules == None:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
546 warning("Couldn't generate RAS for current dataset: " + dataset_name)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
547
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
548 for geni in resolve_rules.values():
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
549 for i, valori in enumerate(geni):
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
550 if valori == None:
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
551 geni[i] = 'None'
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
552
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
553 output_ras = pd.DataFrame.from_dict(resolve_rules)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
554
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
555 output_ras.insert(0, 'Reactions', ids)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
556 output_to_csv = pd.DataFrame.to_csv(output_ras, sep = '\t', index = False)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
557
47
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
558 text_file = open(file, "w")
46
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
559
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
560 text_file.write(output_to_csv)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
561 text_file.close()
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
562
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
563 ############################ MAIN #############################################
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
564
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
565 def main():
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
566 args = process_args(sys.argv)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
567
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
568 if args.rules_selector == 'HMRcore':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
569 recon = pk.load(open(args.tool_dir + '/local/HMRcore_rules.p', 'rb'))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
570 elif args.rules_selector == 'Recon':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
571 recon = pk.load(open(args.tool_dir + '/local/Recon_rules.p', 'rb'))
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
572 elif args.rules_selector == 'Custom':
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
573 ids, rules, gene_in_rule = make_recon(args.custom)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
574
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
575 resolve_none = check_bool(args.none)
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
576
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
577
47
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
578 name = "RAS Dataset"
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
579 dataset = read_dataset(args.input, "dataset")
46
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
580
47
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
581 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
46
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
582
47
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
583 type_gene = gene_type(dataset.iloc[0, 0], name)
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
584
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
585 if args.rules_selector != 'Custom':
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
586 genes = data_gene(dataset, type_gene, name, None)
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
587 ids, rules = load_id_rules(recon.get(type_gene))
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
588 elif args.rules_selector == 'Custom':
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
589 genes = data_gene(dataset, type_gene, name, gene_in_rule)
46
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
590
47
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
591 resolve_rules, err = resolve(genes, rules, ids, resolve_none, name)
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
592
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
593 create_ras(resolve_rules, name, rules, ids, args.ras_output)
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
594
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
595 if err != None and err:
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
596 warning('Warning: gene\n' + str(err) + '\nnot found in class '
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
597 + name + ', the expression level for this gene ' +
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
598 'will be considered NaN\n')
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
599
3af9d394367c Uploaded
bimib
parents: 46
diff changeset
600
46
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
601 print('Execution succeded')
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
602
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
603 return None
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
604
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
605 ###############################################################################
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
606
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
607 if __name__ == "__main__":
5d5d01ef1d68 Uploaded
bimib
parents:
diff changeset
608 main()