Mercurial > repos > iuc > gem_flux_variability_analysis

annotate gem_extract_exchange.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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7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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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
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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3 import cobra
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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4
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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5
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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6 def read_model(model_location):
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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7 model = cobra.io.read_sbml_model(model_location)
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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8 return model
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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9
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7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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11 def get_exchange_reactions_info(model):
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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12 exchange_reactions = model.exchanges
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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13 exchange_reactions_info = []
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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14 for reaction in exchange_reactions:
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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15 exchange_reactions_info.append(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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16 [
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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17 reaction.id,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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18 reaction.name,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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19 reaction.reaction,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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20 reaction.lower_bound,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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21 reaction.upper_bound
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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22 ])
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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23 txt_object = (
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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24 "reaction_id;reaction_name;reaction_stoichiometry;"
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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25 "lower_bound;upper_bound\n"
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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26 )
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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27 for reaction in exchange_reactions_info:
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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28 txt_object += ";".join([str(x) for x in reaction]) + "\n"
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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29 return txt_object
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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30
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31
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32 def __main__():
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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33
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34 # Parsing arguments
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
iuc
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35 parser = argparse.ArgumentParser(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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36 prog="GEM ",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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37 description="This program retrieves the exchange fluxes "
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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38 "of a GEM model to be used in Galaxy.",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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39 epilog="Adding an epilog, but doubt it's needed.",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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40 )
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41 parser.add_argument(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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42 "-m",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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43 "--cb_model_location",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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44 dest="cb_model_location",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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45 action="store",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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46 type=str,
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47 default=None,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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48 required=True,
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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49 help="The model to use."
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50 )
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51 parser.add_argument(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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52 "-output",
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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53 "--output",
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54 dest="out_file",
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55 action="store",
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56 type=str,
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57 default=None,
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58 required=True,
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59 help="The output file."
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60 )
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61 args = parser.parse_args()
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62
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63 # Reading model from file
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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64 try:
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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65 cb_model = read_model(args.cb_model_location)
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66 except Exception as e:
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67 raise Exception(
7c6a05edb3fe planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171
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68 "The model could not be read. Ensure it is in correct SBML format."
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69 ) from e
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70
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71 # Getting exchange reactions info
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72 answer = get_exchange_reactions_info(cb_model)
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73
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74 # Writing exchange reactions info to file
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75 with open(args.out_file, "w") as outfile:
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76 outfile.write(str(answer))
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77
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78
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79 if __name__ == "__main__":
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80 __main__()