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93
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1 from __future__ import division
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2 # galaxy complains this ^^^ needs to be at the very beginning of the file, for some reason.
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3 import sys
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4 import argparse
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5 import collections
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6 import pandas as pd
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7 import pickle as pk
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8 import utils.general_utils as utils
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9 import utils.rule_parsing as ruleUtils
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10 from typing import Union, Optional, List, Dict, Tuple, TypeVar
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309
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11 import os
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93
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12
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13 ERRORS = []
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14 ########################## argparse ##########################################
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15 ARGS :argparse.Namespace
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147
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16 def process_args(args:List[str] = None) -> argparse.Namespace:
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93
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17 """
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18 Processes command-line arguments.
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19
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20 Args:
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21 args (list): List of command-line arguments.
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22
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23 Returns:
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24 Namespace: An object containing parsed arguments.
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25 """
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26 parser = argparse.ArgumentParser(
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27 usage = '%(prog)s [options]',
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28 description = "process some value's genes to create a comparison's map.")
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29
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30 parser.add_argument(
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31 '-rs', '--rules_selector',
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265
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32 type = utils.Model, default = utils.Model.ENGRO2, choices = list(utils.Model),
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93
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33 help = 'chose which type of dataset you want use')
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34
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35 parser.add_argument("-rl", "--rule_list", type = str,
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36 help = "path to input file with custom rules, if provided")
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37
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38 parser.add_argument("-rn", "--rules_name", type = str, help = "custom rules name")
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39 # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in
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40
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41 parser.add_argument(
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42 '-n', '--none',
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43 type = utils.Bool("none"), default = True,
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44 help = 'compute Nan values')
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45
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46 parser.add_argument(
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47 '-td', '--tool_dir',
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48 type = str,
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49 required = True, help = 'your tool directory')
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50
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51 parser.add_argument(
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52 '-ol', '--out_log',
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53 type = str,
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54 help = "Output log")
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55
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56 parser.add_argument(
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57 '-in', '--input', #id รจ diventato in
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58 type = str,
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59 help = 'input dataset')
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60
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61 parser.add_argument(
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62 '-ra', '--ras_output',
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63 type = str,
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64 required = True, help = 'ras output')
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147
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65
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66
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147
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67 return parser.parse_args(args)
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68
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69 ############################ dataset input ####################################
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70 def read_dataset(data :str, name :str) -> pd.DataFrame:
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71 """
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72 Read a dataset from a CSV file and return it as a pandas DataFrame.
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73
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74 Args:
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75 data (str): Path to the CSV file containing the dataset.
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76 name (str): Name of the dataset, used in error messages.
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77
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78 Returns:
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79 pandas.DataFrame: DataFrame containing the dataset.
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80
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81 Raises:
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82 pd.errors.EmptyDataError: If the CSV file is empty.
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83 sys.exit: If the CSV file has the wrong format, the execution is aborted.
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84 """
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85 try:
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86 dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python')
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87 except pd.errors.EmptyDataError:
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88 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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89 if len(dataset.columns) < 2:
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90 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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91 return dataset
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92
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93 ############################ load id e rules ##################################
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94 def load_id_rules(reactions :Dict[str, Dict[str, List[str]]]) -> Tuple[List[str], List[Dict[str, List[str]]]]:
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95 """
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96 Load IDs and rules from a dictionary of reactions.
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97
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98 Args:
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99 reactions (dict): A dictionary where keys are IDs and values are rules.
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100
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101 Returns:
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102 tuple: A tuple containing two lists, the first list containing IDs and the second list containing rules.
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103 """
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104 ids, rules = [], []
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105 for key, value in reactions.items():
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106 ids.append(key)
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107 rules.append(value)
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108 return (ids, rules)
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109
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110 ############################ check_methods ####################################
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111 def gene_type(l :str, name :str) -> str:
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112 """
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113 Determine the type of gene ID.
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114
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115 Args:
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116 l (str): The gene identifier to check.
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117 name (str): The name of the dataset, used in error messages.
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118
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119 Returns:
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120 str: The type of gene ID ('hugo_id', 'ensembl_gene_id', 'symbol', or 'entrez_id').
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121
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122 Raises:
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123 sys.exit: If the gene ID type is not supported, the execution is aborted.
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124 """
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125 if check_hgnc(l):
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126 return 'hugo_id'
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127 elif check_ensembl(l):
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128 return 'ensembl_gene_id'
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129 elif check_symbol(l):
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130 return 'symbol'
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131 elif check_entrez(l):
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132 return 'entrez_id'
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133 else:
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134 sys.exit('Execution aborted:\n' +
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135 'gene ID type in ' + name + ' not supported. Supported ID'+
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136 'types are: HUGO ID, Ensemble ID, HUGO symbol, Entrez ID\n')
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137
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138 def check_hgnc(l :str) -> bool:
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139 """
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140 Check if a gene identifier follows the HGNC format.
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141
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142 Args:
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143 l (str): The gene identifier to check.
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144
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145 Returns:
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146 bool: True if the gene identifier follows the HGNC format, False otherwise.
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147 """
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148 if len(l) > 5:
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149 if (l.upper()).startswith('HGNC:'):
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150 return l[5:].isdigit()
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151 else:
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152 return False
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153 else:
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154 return False
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155
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156 def check_ensembl(l :str) -> bool:
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157 """
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158 Check if a gene identifier follows the Ensembl format.
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159
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160 Args:
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161 l (str): The gene identifier to check.
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162
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163 Returns:
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164 bool: True if the gene identifier follows the Ensembl format, False otherwise.
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165 """
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166 return l.upper().startswith('ENS')
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167
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168
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169 def check_symbol(l :str) -> bool:
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170 """
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171 Check if a gene identifier follows the symbol format.
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172
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173 Args:
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174 l (str): The gene identifier to check.
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175
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176 Returns:
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177 bool: True if the gene identifier follows the symbol format, False otherwise.
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178 """
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179 if len(l) > 0:
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180 if l[0].isalpha() and l[1:].isalnum():
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181 return True
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182 else:
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183 return False
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184 else:
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185 return False
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186
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187 def check_entrez(l :str) -> bool:
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188 """
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189 Check if a gene identifier follows the Entrez ID format.
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190
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191 Args:
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192 l (str): The gene identifier to check.
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193
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194 Returns:
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195 bool: True if the gene identifier follows the Entrez ID format, False otherwise.
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196 """
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197 if len(l) > 0:
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198 return l.isdigit()
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199 else:
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200 return False
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201
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202 ############################ gene #############################################
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203 def data_gene(gene: pd.DataFrame, type_gene: str, name: str, gene_custom: Optional[Dict[str, str]]) -> Dict[str, str]:
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204 """
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205 Process gene data to ensure correct formatting and handle duplicates.
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206
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207 Args:
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208 gene (DataFrame): DataFrame containing gene data.
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209 type_gene (str): Type of gene data (e.g., 'hugo_id', 'ensembl_gene_id', 'symbol', 'entrez_id').
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210 name (str): Name of the dataset.
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211 gene_custom (dict or None): Custom gene data dictionary if provided.
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212
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213 Returns:
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214 dict: A dictionary containing gene data with gene IDs as keys and corresponding values.
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215 """
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309
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216
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93
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217 for i in range(len(gene)):
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218 tmp = gene.iloc[i, 0]
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219 gene.iloc[i, 0] = tmp.strip().split('.')[0]
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220
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221 gene_dup = [item for item, count in
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222 collections.Counter(gene[gene.columns[0]]).items() if count > 1]
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223 pat_dup = [item for item, count in
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224 collections.Counter(list(gene.columns)).items() if count > 1]
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260
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225
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226 gene_in_rule = None
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259
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227
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93
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228 if gene_dup:
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229 if gene_custom == None:
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264
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230
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309
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231 if str(ARGS.rules_selector) == 'HMRcore':
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232 gene_in_rule = pk.load(open(ARGS.tool_dir + '/local/pickle files/HMRcore_genes.p', 'rb'))
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233
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309
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234 elif str(ARGS.rules_selector) == 'Recon':
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235 gene_in_rule = pk.load(open(ARGS.tool_dir + '/local/pickle files/Recon_genes.p', 'rb'))
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93
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236
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309
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237 elif str(ARGS.rules_selector) == 'ENGRO2':
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238 gene_in_rule = pk.load(open(ARGS.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb'))
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263
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239
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309
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240 utils.logWarning(f"{ARGS.tool_dir}'/local/pickle files/ENGRO2_genes.p'", ARGS.out_log)
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259
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241
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93
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242 gene_in_rule = gene_in_rule.get(type_gene)
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243
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244 else:
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245 gene_in_rule = gene_custom
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260
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246
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93
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247 tmp = []
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248 for i in gene_dup:
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249 if gene_in_rule.get(i) == 'ok':
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250 tmp.append(i)
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251 if tmp:
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252 sys.exit('Execution aborted because gene ID '
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253 +str(tmp)+' in '+name+' is duplicated\n')
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254
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255 if pat_dup: utils.logWarning(f"Warning: duplicated label\n{pat_dup} in {name}", ARGS.out_log)
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256 return (gene.set_index(gene.columns[0])).to_dict()
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257
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258 ############################ resolve ##########################################
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259 def replace_gene_value(l :str, d :str) -> Tuple[Union[int, float], list]:
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260 """
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261 Replace gene identifiers with corresponding values from a dictionary.
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262
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263 Args:
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264 l (str): String of gene identifier.
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265 d (str): String corresponding to its value.
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266
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267 Returns:
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268 tuple: A tuple containing two lists: the first list contains replaced values, and the second list contains any errors encountered during replacement.
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269 """
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270 tmp = []
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271 err = []
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272 while l:
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273 if isinstance(l[0], list):
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274 tmp_rules, tmp_err = replace_gene_value(l[0], d)
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275 tmp.append(tmp_rules)
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276 err.extend(tmp_err)
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277 else:
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278 value = replace_gene(l[0], d)
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279 tmp.append(value)
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280 if value == None:
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281 err.append(l[0])
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282 l = l[1:]
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283 return (tmp, err)
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284
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285 def replace_gene(l :str, d :str) -> Union[int, float]:
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286 """
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287 Replace a single gene identifier with its corresponding value from a dictionary.
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288
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289 Args:
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290 l (str): Gene identifier to replace.
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291 d (str): String corresponding to its value.
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292
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293 Returns:
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294 float/int: Corresponding value from the dictionary if found, None otherwise.
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295
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296 Raises:
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297 sys.exit: If the value associated with the gene identifier is not valid.
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298 """
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299 if l =='and' or l == 'or':
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300 return l
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301 else:
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302 value = d.get(l, None)
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303 if not(value == None or isinstance(value, (int, float))):
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304 sys.exit('Execution aborted: ' + value + ' value not valid\n')
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305 return value
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306
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307 T = TypeVar("T", bound = Optional[Union[int, float]])
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308 def computes(val1 :T, op :str, val2 :T, cn :bool) -> T:
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309 """
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310 Compute the RAS value between two value and an operator ('and' or 'or').
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311
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312 Args:
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313 val1(Optional(Union[float, int])): First value.
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314 op (str): Operator ('and' or 'or').
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315 val2(Optional(Union[float, int])): Second value.
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316 cn (bool): Control boolean value.
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317
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318 Returns:
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319 Optional(Union[float, int]): Result of the computation.
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320 """
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321 if val1 != None and val2 != None:
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322 if op == 'and':
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323 return min(val1, val2)
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324 else:
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325 return val1 + val2
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326 elif op == 'and':
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327 if cn is True:
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328 if val1 != None:
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329 return val1
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330 elif val2 != None:
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331 return val2
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332 else:
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333 return None
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334 else:
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335 return None
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336 else:
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337 if val1 != None:
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338 return val1
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339 elif val2 != None:
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340 return val2
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341 else:
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342 return None
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343
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344 # ris should be Literal[None] but Literal is not supported in Python 3.7
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345 def control(ris, l :List[Union[int, float, list]], cn :bool) -> Union[bool, int, float]: #Union[Literal[False], int, float]:
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346 """
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347 Control the format of the expression.
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348
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349 Args:
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350 ris: Intermediate result.
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351 l (list): Expression to control.
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352 cn (bool): Control boolean value.
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353
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354 Returns:
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355 Union[Literal[False], int, float]: Result of the control.
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356 """
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357 if len(l) == 1:
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358 if isinstance(l[0], (float, int)) or l[0] == None:
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359 return l[0]
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360 elif isinstance(l[0], list):
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361 return control(None, l[0], cn)
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362 else:
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363 return False
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364 elif len(l) > 2:
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365 return control_list(ris, l, cn)
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366 else:
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367 return False
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368
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369 def control_list(ris, l :List[Optional[Union[float, int, list]]], cn :bool) -> Optional[bool]: #Optional[Literal[False]]:
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370 """
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371 Control the format of a list of expressions.
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372
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373 Args:
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374 ris: Intermediate result.
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375 l (list): List of expressions to control.
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376 cn (bool): Control boolean value.
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377
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378 Returns:
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379 Optional[Literal[False]]: Result of the control.
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380 """
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381 while l:
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382 if len(l) == 1:
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383 return False
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384 elif (isinstance(l[0], (float, int)) or
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385 l[0] == None) and l[1] in ['and', 'or']:
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386 if isinstance(l[2], (float, int)) or l[2] == None:
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387 ris = computes(l[0], l[1], l[2], cn)
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388 elif isinstance(l[2], list):
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389 tmp = control(None, l[2], cn)
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390 if tmp is False:
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391 return False
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392 else:
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393 ris = computes(l[0], l[1], tmp, cn)
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394 else:
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395 return False
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396 l = l[3:]
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397 elif l[0] in ['and', 'or']:
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398 if isinstance(l[1], (float, int)) or l[1] == None:
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399 ris = computes(ris, l[0], l[1], cn)
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400 elif isinstance(l[1], list):
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401 tmp = control(None,l[1], cn)
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402 if tmp is False:
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403 return False
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404 else:
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405 ris = computes(ris, l[0], tmp, cn)
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406 else:
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407 return False
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408 l = l[2:]
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409 elif isinstance(l[0], list) and l[1] in ['and', 'or']:
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410 if isinstance(l[2], (float, int)) or l[2] == None:
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411 tmp = control(None, l[0], cn)
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412 if tmp is False:
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413 return False
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414 else:
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415 ris = computes(tmp, l[1], l[2], cn)
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416 elif isinstance(l[2], list):
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417 tmp = control(None, l[0], cn)
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418 tmp2 = control(None, l[2], cn)
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419 if tmp is False or tmp2 is False:
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420 return False
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421 else:
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422 ris = computes(tmp, l[1], tmp2, cn)
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423 else:
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424 return False
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425 l = l[3:]
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426 else:
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427 return False
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428 return ris
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429
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430 ResolvedRules = Dict[str, List[Optional[Union[float, int]]]]
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431 def resolve(genes: Dict[str, str], rules: List[str], ids: List[str], resolve_none: bool, name: str) -> Tuple[Optional[ResolvedRules], Optional[list]]:
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432 """
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433 Resolve rules using gene data to compute scores for each rule.
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434
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435 Args:
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436 genes (dict): Dictionary containing gene data with gene IDs as keys and corresponding values.
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437 rules (list): List of rules to resolve.
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438 ids (list): List of IDs corresponding to the rules.
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439 resolve_none (bool): Flag indicating whether to resolve None values in the rules.
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440 name (str): Name of the dataset.
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441
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442 Returns:
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443 tuple: A tuple containing resolved rules as a dictionary and a list of gene IDs not found in the data.
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444 """
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445 resolve_rules = {}
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446 not_found = []
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447 flag = False
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448 for key, value in genes.items():
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449 tmp_resolve = []
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450 for i in range(len(rules)):
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451 tmp = rules[i]
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452 if tmp:
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453 tmp, err = replace_gene_value(tmp, value)
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454 if err:
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455 not_found.extend(err)
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456 ris = control(None, tmp, resolve_none)
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457 if ris is False or ris == None:
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458 tmp_resolve.append(None)
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459 else:
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460 tmp_resolve.append(ris)
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461 flag = True
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462 else:
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463 tmp_resolve.append(None)
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464 resolve_rules[key] = tmp_resolve
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465
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466 if flag is False:
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467 utils.logWarning(
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468 f"Warning: no computable score (due to missing gene values) for class {name}, the class has been disregarded",
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469 ARGS.out_log)
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470
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|
471 return (None, None)
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472
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|
473 return (resolve_rules, list(set(not_found)))
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|
474 ############################ create_ras #######################################
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475 def create_ras(resolve_rules: Optional[ResolvedRules], dataset_name: str, rules: List[str], ids: List[str], file: str) -> None:
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476 """
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|
|
477 Create a RAS (Reaction Activity Score) file from resolved rules.
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|
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478
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|
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479 Args:
|
|
|
480 resolve_rules (dict): Dictionary containing resolved rules.
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|
|
481 dataset_name (str): Name of the dataset.
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|
482 rules (list): List of rules.
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|
|
483 file (str): Path to the output RAS file.
|
|
|
484
|
|
|
485 Returns:
|
|
|
486 None
|
|
|
487 """
|
|
|
488 if resolve_rules is None:
|
|
|
489 utils.logWarning(f"Couldn't generate RAS for current dataset: {dataset_name}", ARGS.out_log)
|
|
|
490
|
|
|
491 for geni in resolve_rules.values():
|
|
|
492 for i, valori in enumerate(geni):
|
|
|
493 if valori == None:
|
|
|
494 geni[i] = 'None'
|
|
|
495
|
|
|
496 output_ras = pd.DataFrame.from_dict(resolve_rules)
|
|
|
497
|
|
|
498 output_ras.insert(0, 'Reactions', ids)
|
|
|
499 output_to_csv = pd.DataFrame.to_csv(output_ras, sep = '\t', index = False)
|
|
|
500
|
|
|
501 text_file = open(file, "w")
|
|
|
502
|
|
|
503 text_file.write(output_to_csv)
|
|
|
504 text_file.close()
|
|
|
505
|
|
|
506 ################################- NEW RAS COMPUTATION -################################
|
|
|
507 Expr = Optional[Union[int, float]]
|
|
|
508 Ras = Expr
|
|
|
509 def ras_for_cell_lines(dataset: pd.DataFrame, rules: Dict[str, ruleUtils.OpList]) -> Dict[str, Dict[str, Ras]]:
|
|
|
510 """
|
|
|
511 Generates the RAS scores for each cell line found in the dataset.
|
|
|
512
|
|
|
513 Args:
|
|
|
514 dataset (pd.DataFrame): Dataset containing gene values.
|
|
|
515 rules (dict): The dict containing reaction ids as keys and rules as values.
|
|
|
516
|
|
|
517 Side effects:
|
|
|
518 dataset : mut
|
|
|
519
|
|
|
520 Returns:
|
|
|
521 dict: A dictionary where each key corresponds to a cell line name and each value is a dictionary
|
|
|
522 where each key corresponds to a reaction ID and each value is its computed RAS score.
|
|
|
523 """
|
|
|
524 ras_values_by_cell_line = {}
|
|
|
525 dataset.set_index(dataset.columns[0], inplace=True)
|
|
|
526 # Considera tutte le colonne tranne la prima in cui ci sono gli hugo quindi va scartata
|
|
|
527 for cell_line_name in dataset.columns[1:]:
|
|
|
528 cell_line = dataset[cell_line_name].to_dict()
|
|
|
529 ras_values_by_cell_line[cell_line_name]= get_ras_values(rules, cell_line)
|
|
|
530 return ras_values_by_cell_line
|
|
|
531
|
|
|
532 def get_ras_values(value_rules: Dict[str, ruleUtils.OpList], dataset: Dict[str, Expr]) -> Dict[str, Ras]:
|
|
|
533 """
|
|
|
534 Computes the RAS (Reaction Activity Score) values for each rule in the given dict.
|
|
|
535
|
|
|
536 Args:
|
|
|
537 value_rules (dict): A dictionary where keys are reaction ids and values are OpLists.
|
|
|
538 dataset : gene expression data of one cell line.
|
|
|
539
|
|
|
540 Returns:
|
|
|
541 dict: A dictionary where keys are reaction ids and values are the computed RAS values for each rule.
|
|
|
542 """
|
|
|
543 return {key: ras_op_list(op_list, dataset) for key, op_list in value_rules.items()}
|
|
|
544
|
|
|
545 def get_gene_expr(dataset :Dict[str, Expr], name :str) -> Expr:
|
|
|
546 """
|
|
|
547 Extracts the gene expression of the given gene from a cell line dataset.
|
|
|
548
|
|
|
549 Args:
|
|
|
550 dataset : gene expression data of one cell line.
|
|
|
551 name : gene name.
|
|
|
552
|
|
|
553 Returns:
|
|
|
554 Expr : the gene's expression value.
|
|
|
555 """
|
|
|
556 expr = dataset.get(name, None)
|
|
|
557 if expr is None: ERRORS.append(name)
|
|
|
558
|
|
|
559 return expr
|
|
|
560
|
|
|
561 def ras_op_list(op_list: ruleUtils.OpList, dataset: Dict[str, Expr]) -> Ras:
|
|
|
562 """
|
|
|
563 Computes recursively the RAS (Reaction Activity Score) value for the given OpList, considering the specified flag to control None behavior.
|
|
|
564
|
|
|
565 Args:
|
|
|
566 op_list (OpList): The OpList representing a rule with gene values.
|
|
|
567 dataset : gene expression data of one cell line.
|
|
|
568
|
|
|
569 Returns:
|
|
|
570 Ras: The computed RAS value for the given OpList.
|
|
|
571 """
|
|
|
572 op = op_list.op
|
|
|
573 ras_value :Ras = None
|
|
|
574 if not op: return get_gene_expr(dataset, op_list[0])
|
|
|
575 if op is ruleUtils.RuleOp.AND and not ARGS.none and None in op_list: return None
|
|
|
576
|
|
|
577 for i in range(len(op_list)):
|
|
|
578 item = op_list[i]
|
|
|
579 if isinstance(item, ruleUtils.OpList):
|
|
|
580 item = ras_op_list(item, dataset)
|
|
|
581
|
|
|
582 else:
|
|
|
583 item = get_gene_expr(dataset, item)
|
|
|
584
|
|
|
585 if item is None:
|
|
|
586 if op is ruleUtils.RuleOp.AND and not ARGS.none: return None
|
|
|
587 continue
|
|
|
588
|
|
|
589 if ras_value is None:
|
|
|
590 ras_value = item
|
|
|
591 else:
|
|
|
592 ras_value = ras_value + item if op is ruleUtils.RuleOp.OR else min(ras_value, item)
|
|
|
593
|
|
|
594 return ras_value
|
|
|
595
|
|
|
596 def save_as_tsv(rasScores: Dict[str, Dict[str, Ras]], reactions :List[str]) -> None:
|
|
|
597 """
|
|
|
598 Save computed ras scores to the given path, as a tsv file.
|
|
|
599
|
|
|
600 Args:
|
|
|
601 rasScores : the computed ras scores.
|
|
|
602 path : the output tsv file's path.
|
|
|
603
|
|
|
604 Returns:
|
|
|
605 None
|
|
|
606 """
|
|
|
607 for scores in rasScores.values(): # this is actually a lot faster than using the ootb dataframe metod, sadly
|
|
|
608 for reactId, score in scores.items():
|
|
|
609 if score is None: scores[reactId] = "None"
|
|
|
610
|
|
|
611 output_ras = pd.DataFrame.from_dict(rasScores)
|
|
|
612 output_ras.insert(0, 'Reactions', reactions)
|
|
|
613 output_ras.to_csv(ARGS.ras_output, sep = '\t', index = False)
|
|
|
614
|
|
|
615 ############################ MAIN #############################################
|
|
|
616 #TODO: not used but keep, it will be when the new translator dicts will be used.
|
|
|
617 def translateGene(geneName :str, encoding :str, geneTranslator :Dict[str, Dict[str, str]]) -> str:
|
|
|
618 """
|
|
|
619 Translate gene from any supported encoding to HugoID.
|
|
|
620
|
|
|
621 Args:
|
|
|
622 geneName (str): the name of the gene in its current encoding.
|
|
|
623 encoding (str): the encoding.
|
|
|
624 geneTranslator (Dict[str, Dict[str, str]]): the dict containing all supported gene names
|
|
|
625 and encodings in the current model, mapping each to the corresponding HugoID encoding.
|
|
|
626
|
|
|
627 Raises:
|
|
|
628 ValueError: When the gene isn't supported in the model.
|
|
|
629
|
|
|
630 Returns:
|
|
|
631 str: the gene in HugoID encoding.
|
|
|
632 """
|
|
|
633 supportedGenesInEncoding = geneTranslator[encoding]
|
|
|
634 if geneName in supportedGenesInEncoding: return supportedGenesInEncoding[geneName]
|
|
|
635 raise ValueError(f"Gene \"{geneName}\" non trovato, verifica di star utilizzando il modello corretto!")
|
|
|
636
|
|
|
637 def load_custom_rules() -> Dict[str, ruleUtils.OpList]:
|
|
|
638 """
|
|
|
639 Opens custom rules file and extracts the rules. If the file is in .csv format an additional parsing step will be
|
|
|
640 performed, significantly impacting the runtime.
|
|
|
641
|
|
|
642 Returns:
|
|
|
643 Dict[str, ruleUtils.OpList] : dict mapping reaction IDs to rules.
|
|
|
644 """
|
|
|
645 datFilePath = utils.FilePath.fromStrPath(ARGS.rule_list) # actual file, stored in galaxy as a .dat
|
|
|
646
|
|
|
647 try: filenamePath = utils.FilePath.fromStrPath(ARGS.rules_name) # file's name in input, to determine its original ext
|
|
|
648 except utils.PathErr as err:
|
|
|
649 raise utils.PathErr(filenamePath, f"Please make sure your file's name is a valid file path, {err.msg}")
|
|
|
650
|
|
|
651 if filenamePath.ext is utils.FileFormat.PICKLE: return utils.readPickle(datFilePath)
|
|
|
652
|
|
|
653 # csv rules need to be parsed, those in a pickle format are taken to be pre-parsed.
|
|
|
654 return { line[0] : ruleUtils.parseRuleToNestedList(line[1]) for line in utils.readCsv(datFilePath) }
|
|
|
655
|
|
147
|
656 def main(args:List[str] = None) -> None:
|
|
93
|
657 """
|
|
|
658 Initializes everything and sets the program in motion based on the fronted input arguments.
|
|
|
659
|
|
|
660 Returns:
|
|
|
661 None
|
|
|
662 """
|
|
|
663 # get args from frontend (related xml)
|
|
|
664 global ARGS
|
|
147
|
665 ARGS = process_args(args)
|
|
309
|
666
|
|
93
|
667 # read dataset
|
|
|
668 dataset = read_dataset(ARGS.input, "dataset")
|
|
|
669 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
|
|
|
670
|
|
|
671 # remove versioning from gene names
|
|
|
672 dataset.iloc[:, 0] = dataset.iloc[:, 0].str.split('.').str[0]
|
|
|
673
|
|
|
674 # handle custom models
|
|
|
675 model :utils.Model = ARGS.rules_selector
|
|
309
|
676
|
|
93
|
677 if model is utils.Model.Custom:
|
|
|
678 rules = load_custom_rules()
|
|
|
679 reactions = list(rules.keys())
|
|
|
680
|
|
|
681 save_as_tsv(ras_for_cell_lines(dataset, rules), reactions)
|
|
|
682 if ERRORS: utils.logWarning(
|
|
|
683 f"The following genes are mentioned in the rules but don't appear in the dataset: {ERRORS}",
|
|
|
684 ARGS.out_log)
|
|
|
685
|
|
|
686 return
|
|
|
687
|
|
|
688 # This is the standard flow of the ras_generator program, for non-custom models.
|
|
|
689 name = "RAS Dataset"
|
|
|
690 type_gene = gene_type(dataset.iloc[0, 0], name)
|
|
|
691
|
|
|
692 rules = model.getRules(ARGS.tool_dir)
|
|
|
693 genes = data_gene(dataset, type_gene, name, None)
|
|
|
694 ids, rules = load_id_rules(rules.get(type_gene))
|
|
|
695
|
|
|
696 resolve_rules, err = resolve(genes, rules, ids, ARGS.none, name)
|
|
|
697 create_ras(resolve_rules, name, rules, ids, ARGS.ras_output)
|
|
|
698
|
|
|
699 if err: utils.logWarning(
|
|
|
700 f"Warning: gene(s) {err} not found in class \"{name}\", " +
|
|
|
701 "the expression level for this gene will be considered NaN",
|
|
|
702 ARGS.out_log)
|
|
|
703
|
|
|
704 print("Execution succeded")
|
|
|
705
|
|
|
706 ###############################################################################
|
|
|
707 if __name__ == "__main__":
|
|
309
|
708 main()
|
