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1 import os
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2 import csv
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3 import cobra
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4 import pickle
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5 import argparse
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6 import pandas as pd
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7 import utils.general_utils as utils
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8 import utils.rule_parsing as rulesUtils
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9 from typing import Optional, Tuple, Union, Dict
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10 import utils.reaction_parsing as reactionUtils
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11
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12 ARGS : argparse.Namespace
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13 def process_args() -> argparse.Namespace:
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14 """
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15 Interfaces the script of a module with its frontend, making the user's choices for
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16 various parameters available as values in code.
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17
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18 Args:
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19 args : Always obtained (in file) from sys.argv
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20
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21 Returns:
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22 Namespace : An object containing the parsed arguments
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23 """
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24 parser = argparse.ArgumentParser(
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25 usage = "%(prog)s [options]",
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26 description = "generate custom data from a given model")
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27
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28 parser.add_argument("-ol", "--out_log", type = str, required = True, help = "Output log")
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29 parser.add_argument("-id", "--input", type = str, required = True, help = "Input model")
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30 parser.add_argument("-mn", "--name", type = str, required = True, help = "Input model name")
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31 # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in
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32
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33 parser.add_argument(
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34 "-of", "--output_format",
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35 # vvv I have to use .fromExt because enums in python are the plague and have been implemented by a chimpanzee.
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36 type = utils.FileFormat.fromExt, default = utils.FileFormat.PICKLE,
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37 choices = [utils.FileFormat.CSV, utils.FileFormat.PICKLE],
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38 # ^^^ Not all variants are valid here, otherwise list(utils.FileFormat) would be best.
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39 required = True, help = "Extension of all output files")
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40
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41 argsNamespace = parser.parse_args()
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42 argsNamespace.out_dir = "result"
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43 # ^ can't get this one to work from xml, there doesn't seem to be a way to get the directory attribute from the collection
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44
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45 return argsNamespace
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46
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47 ################################- INPUT DATA LOADING -################################
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48 def load_custom_model(file_path :utils.FilePath, ext :Optional[utils.FileFormat] = None) -> cobra.Model:
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49 """
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50 Loads a custom model from a file, either in JSON or XML format.
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51
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52 Args:
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53 file_path : The path to the file containing the custom model.
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54 ext : explicit file extension. Necessary for standard use in galaxy because of its weird behaviour.
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55
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56 Raises:
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57 DataErr : if the file is in an invalid format or cannot be opened for whatever reason.
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58
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59 Returns:
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60 cobra.Model : the model, if successfully opened.
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61 """
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62 ext = ext if ext else file_path.ext
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63 try:
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64 if ext is utils.FileFormat.XML:
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65 return cobra.io.read_sbml_model(file_path.show())
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66
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67 if ext is utils.FileFormat.JSON:
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68 return cobra.io.load_json_model(file_path.show())
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69
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70 except Exception as e: raise utils.DataErr(file_path, e.__str__())
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71 raise utils.DataErr(file_path,
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72 f"Formato \"{file_path.ext}\" non riconosciuto, sono supportati solo file JSON e XML")
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73
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74 ################################- DATA GENERATION -################################
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75 ReactionId = str
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76 def generate_rules(model: cobra.Model, *, asParsed = True) -> Union[Dict[ReactionId, rulesUtils.OpList], Dict[ReactionId, str]]:
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77 """
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78 Generates a dictionary mapping reaction ids to rules from the model.
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79
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80 Args:
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81 model : the model to derive data from.
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82 asParsed : if True parses the rules to an optimized runtime format, otherwise leaves them as strings.
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83
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84 Returns:
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85 Dict[ReactionId, rulesUtils.OpList] : the generated dictionary of parsed rules.
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86 Dict[ReactionId, str] : the generated dictionary of raw rules.
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87 """
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88 # Is the below approach convoluted? yes
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89 # Ok but is it inefficient? probably
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90 # Ok but at least I don't have to repeat the check at every rule (I'm clinically insane)
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91 _ruleGetter = lambda reaction : reaction.gene_reaction_rule
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92 ruleExtractor = (lambda reaction :
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93 rulesUtils.parseRuleToNestedList(_ruleGetter(reaction))) if asParsed else _ruleGetter
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94
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95 return {
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96 reaction.id : ruleExtractor(reaction)
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97 for reaction in model.reactions
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98 if reaction.gene_reaction_rule }
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99
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100 def generate_reactions(model :cobra.Model, *, asParsed = True) -> Dict[ReactionId, str]:
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101 """
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102 Generates a dictionary mapping reaction ids to reaction formulas from the model.
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103
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104 Args:
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105 model : the model to derive data from.
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106 asParsed : if True parses the reactions to an optimized runtime format, otherwise leaves them as they are.
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107
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108 Returns:
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109 Dict[ReactionId, str] : the generated dictionary.
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110 """
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111
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112 unparsedReactions = {
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113 reaction.id : reaction.reaction
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114 for reaction in model.reactions
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115 if reaction.reaction
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116 }
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117
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118 if not asParsed: return unparsedReactions
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119
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120 return reactionUtils.create_reaction_dict(unparsedReactions)
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121
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122 def get_medium(model:cobra.Model) -> pd.DataFrame:
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123 trueMedium=[]
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124 for r in model.reactions:
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125 positiveCoeff=0
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126 for m in r.metabolites:
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127 if r.get_coefficient(m.id)>0:
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128 positiveCoeff=1;
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129 if (positiveCoeff==0 and r.lower_bound<0):
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130 trueMedium.append(r.id)
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131
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132 df_medium = pd.DataFrame()
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133 df_medium["reaction"] = trueMedium
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134 return df_medium
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135
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136 def generate_bounds(model:cobra.Model) -> pd.DataFrame:
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137
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138 rxns = []
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139 for reaction in model.reactions:
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140 rxns.append(reaction.id)
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141
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142 bounds = pd.DataFrame(columns = ["lower_bound", "upper_bound"], index=rxns)
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143
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144 for reaction in model.reactions:
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145 bounds.loc[reaction.id] = [reaction.lower_bound, reaction.upper_bound]
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146 return bounds
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147
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148
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149 ###############################- FILE SAVING -################################
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150 def save_as_csv(data :dict, file_path :utils.FilePath, fieldNames :Tuple[str, str]) -> None:
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151 """
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152 Saves any dictionary-shaped data in a .csv file created at the given file_path.
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153
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154 Args:
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155 data : the data to be written to the file.
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156 file_path : the path to the .csv file.
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157 fieldNames : the names of the fields (columns) in the .csv file.
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158
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159 Returns:
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160 None
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161 """
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162 with open(file_path.show(), 'w', newline='') as csvfile:
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163 writer = csv.DictWriter(csvfile, fieldnames = fieldNames)
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164 writer.writeheader()
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165
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166 for key, value in data.items():
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167 writer.writerow({ fieldNames[0] : key, fieldNames[1] : value })
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168
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169 ###############################- ENTRY POINT -################################
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170 def main() -> None:
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171 """
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172 Initializes everything and sets the program in motion based on the fronted input arguments.
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173
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174 Returns:
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175 None
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176 """
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177 # get args from frontend (related xml)
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178 global ARGS
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179 ARGS = process_args()
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180
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181 # this is the worst thing I've seen so far, congrats to the former MaREA devs for suggesting this!
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182 if os.path.isdir(ARGS.out_dir) == False: os.makedirs(ARGS.out_dir)
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183
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184 # load custom model
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185 model = load_custom_model(
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186 utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.name).ext)
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187
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188 # generate data and save it in the desired format and in a location galaxy understands
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189 # (it should show up as a collection in the history)
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190 rulesPath = utils.FilePath("rules", ARGS.output_format, prefix = ARGS.out_dir)
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191 reactionsPath = utils.FilePath("reactions", ARGS.output_format, prefix = ARGS.out_dir)
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192 boundsPath = utils.FilePath("bounds", ARGS.output_format, prefix = ARGS.out_dir)
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193 mediumPath = utils.FilePath("medium", ARGS.output_format, prefix = ARGS.out_dir)
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194
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195 if ARGS.output_format is utils.FileFormat.PICKLE:
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196 rules = generate_rules(model, asParsed = True)
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197 reactions = generate_reactions(model, asParsed = True)
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198 bounds = generate_bounds(model)
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199 medium = get_medium(model)
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200 utils.writePickle(rulesPath, rules)
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201 utils.writePickle(reactionsPath, reactions)
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202 utils.writePickle(boundsPath, bounds)
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203 utils.writePickle(mediumPath, medium)
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204 bounds.to_pickle(boundsPath.show())
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205 medium.to_pickle(mediumPath.show())
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206
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207 elif ARGS.output_format is utils.FileFormat.CSV:
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208 rules = generate_rules(model, asParsed = False)
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209 reactions = generate_reactions(model, asParsed = False)
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210 bounds = generate_bounds(model)
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211 medium = get_medium(model)
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212 save_as_csv(rules, rulesPath, ("ReactionID", "Rule"))
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213 save_as_csv(reactions, reactionsPath, ("ReactionID", "Reaction"))
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214 bounds.to_csv(boundsPath.show())
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215 medium.to_csv(mediumPath.show())
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216
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217
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218 # ^ Please if anyone works on this after updating python to 3.12 change the if/elif into a match statement!!
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219
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220 if __name__ == '__main__':
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221 main() |
