Mercurial > repos > iuc > gem_flux_variability_analysis

annotate gem_flux_variability_analysis.py @ 0:7c6a05edb3fe draft default tip

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planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
author iuc
date Fri, 13 Dec 2024 21:32:00 +0000
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0
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
parents:
diff changeset
1 import argparse
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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2
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iuc
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3 import cobra
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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4 import pandas as pd
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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5
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iuc
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6
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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7 def __main__():
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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8 parser = argparse.ArgumentParser(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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9 prog="FluxVariabilityAnalysis",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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10 description="This program performs flux variability "
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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11 "analysis on a GEM",
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iuc
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12 epilog="Adding an epilog, but doubt it's needed.",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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13 )
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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14 parser.add_argument(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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15 "-m", "--cb_model_location",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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16 dest="cb_model_location",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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17 action="store",
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18 type=str,
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19 default=None,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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20 required=True,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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21 help="The model to use."
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22 )
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iuc
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23 parser.add_argument(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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24 "-output",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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25 "--output",
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26 dest="out_file",
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27 action="store",
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28 type=str,
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29 default=None,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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30 required=True,
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31 help="The output file."
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32 )
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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33 parser.add_argument(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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34 "-f",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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35 "--fraction",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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36 dest="fraction_of_optimum",
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37 action="store",
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38 type=float,
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39 default=None,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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40 required=True,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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41 help="The fraction of optimum the FVA solutions should come within."
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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42 )
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43 parser.add_argument(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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44 "-u",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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45 "--uptake_constraints_file",
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46 dest="uptake_constraints_file",
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47 action="store",
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48 type=str,
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49 default=None,
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50 required=False,
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51 help="File containing new uptake constraits."
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52 )
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53
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54 args = parser.parse_args()
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55
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56 # Validate constraints file first if provided
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57 constraints_df = None
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58 if args.uptake_constraints_file is not None\
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59 and args.uptake_constraints_file != "None":
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60 try:
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61 constraints_df = pd.read_csv(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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62 args.uptake_constraints_file,
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63 sep=";",
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64 header=0,
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65 index_col=False
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66 )
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67
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68 required_columns = ['reaction_id', 'lower_bound', 'upper_bound']
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69 missing_columns = [col for col in required_columns if
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70 col not in constraints_df.columns]
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71
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72 if missing_columns:
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73 raise ValueError(
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74 f"Constraints file is missing required columns: "
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75 f"{', '.join(missing_columns)}. "
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76 f"Required columns are: {', '.join(required_columns)}"
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77 )
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78 except FileNotFoundError:
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79 raise FileNotFoundError(
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80 f"Constraints file not found: {args.uptake_constraints_file}"
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81 )
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82 except pd.errors.EmptyDataError:
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83 raise ValueError("Constraints file is empty")
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84 except Exception as e:
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85 raise ValueError(f"Error processing constraints file: {str(e)}")
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86
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87 # Load model
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88 cb_model = cobra.io.read_sbml_model(args.cb_model_location)
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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89
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90 # Apply constraints if they were loaded successfully
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91 if constraints_df is not None:
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92 for index, row in constraints_df.iterrows():
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93 cb_model.reactions.get_by_id(
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94 row["reaction_id"]).lower_bound = float(row["lower_bound"])
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95 cb_model.reactions.get_by_id(
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96 row["reaction_id"]).upper_bound = float(row["upper_bound"])
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97
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98 fraction_of_optimum = args.fraction_of_optimum
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99
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100 # perform fva
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101 fva_result = cobra.flux_analysis.flux_variability_analysis(
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102 cb_model,
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103 fraction_of_optimum=fraction_of_optimum
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104 )
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105
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106 # add reaction names and ids to the dataframe
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107 fva_result["reaction_id"] = fva_result.index
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108 fva_result["reaction_name"] = fva_result["reaction_id"].apply(
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109 lambda x: cb_model.reactions.get_by_id(x).name
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110 )
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111
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112 # reorder the columns
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113 fva_result = fva_result[[
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114 "reaction_id", "reaction_name", "minimum", "maximum"
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115 ]]
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116
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117 fva_result.to_csv(args.out_file, sep=";", index=False, header=True)
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118
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119
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120 if __name__ == "__main__":
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121 __main__()