Mercurial > repos > tduigou > get_sbml_model

annotate get_infos.py @ 11:062f51695ae0 draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 8ab0b9452a029b409b18b80243958b4901bdeb3d
author tduigou
date Tue, 01 Apr 2025 09:59:21 +0000
parents dc1167469d62
children 1aadcfdae10b
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1 from argparse import ArgumentParser
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dc1167469d62 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343
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2 from libsbml import readSBMLFromFile
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3 from taxonid import get_taxonid
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4 from requests import get as r_get
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6
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7 def get_biomass_rxn(sbml_doc):
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8 """
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9 Returns the biomass reaction of the model
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10
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11 Parameters
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12 ----------
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13 sbml_doc: libsbml.SBMLDocument
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14 SBML model
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16 Returns
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17 -------
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18 biomass_rxn: libsbml.Reaction
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19 Biomass reaction
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20 """
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21 reactions = sbml_doc.getModel().getListOfReactions()
768ed7cc0978 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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22 # Search for 'biomass' keyword in reaction name
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23 for rxn in reactions:
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24 if "biomass" in rxn.getName().lower():
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25 return rxn
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26 # Search for 'biomass' keyword in products
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27 # AND not in reactants
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28 for rxn in reactions:
768ed7cc0978 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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29 in_reactants = False
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30 for reac in rxn.getListOfReactants():
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31 if "biomass" in reac.getSpecies().lower():
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32 in_reactants = True
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33 break
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34 if not in_reactants:
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35 for prod in rxn.getListOfProducts():
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36 if "biomass" in prod.getSpecies().lower():
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37 return rxn
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38 return None
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41 def args():
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42 parser = ArgumentParser("Returns cell informations")
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43 parser.add_argument("infile", type=str, help="SBML input file (xml)")
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44 parser.add_argument("--biomassid", type=str, help="ID of biomass reaction")
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45 parser.add_argument("--taxonid", type=str, help="Taxonomy ID")
062f51695ae0 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 8ab0b9452a029b409b18b80243958b4901bdeb3d
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46 parser.add_argument("--standalone", action="store_true", help="Standalone mode, e.g. do not retrieve taxonomy ID on Internet (true if --taxonid is provided)")
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47 parser.add_argument("--compartments-outfile", type=str, help="Path to store cell compartments")
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48 parser.add_argument("--biomassid-outfile", type=str, help="Path to store biomass reaction ID")
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49 parser.add_argument("--taxonid-outfile", type=str, help="Path to store host taxonomy ID")
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50 params = parser.parse_args()
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51 return params
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53
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54 def get_organism_from_bigg_model(model_id):
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55 """Try to retrieve organism info from BiGG Models for a given model ID."""
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56 url = f"http://bigg.ucsd.edu/api/v2/models/{model_id}"
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57 try:
dc1167469d62 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343
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58 response = r_get(url)
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59 if response.status_code == 200:
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60 data = response.json()
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61 organism = data.get("organism")
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62 return organism
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63 except Exception as e:
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64 print(f"Error querying BiGG: {e}")
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65 return None
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66
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67 def get_taxon_id(input_name):
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68 """Try BiGG model name first, then NCBI directly."""
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69 print(f"Trying input: {input_name}")
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70
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71 # Try resolving as a BiGG model
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72 organism = get_organism_from_bigg_model(input_name)
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73 if organism:
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74 print(f"Model '{input_name}' maps to organism: {organism}")
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75 taxon_id = get_taxonid(organism)
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76 if taxon_id:
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77 return taxon_id
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78
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79 # If not a model, try directly as an organism name
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80 print(f"Trying NCBI search with input: {input_name}")
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81 return get_taxonid(input_name)
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83
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84 def entry_point():
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85 params = args()
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86
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87 # test if the file exists
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88 with open(params.infile):
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89 pass
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91 sbml_doc = readSBMLFromFile(params.infile)
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92
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93 compartments = sbml_doc.getModel().getListOfCompartments()
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94 comp_str = ""
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95 for comp in compartments:
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96 comp_str += f"{comp.getId()}\t{comp.getName()}\n"
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97 print("Compartments:")
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98 for comp in compartments:
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99 print(f"{comp.getId()}\t{comp.getName()}".replace("\n", " | "))
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100 if params.compartments_outfile:
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101 with open(params.compartments_outfile, "w") as f:
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102 f.write("#ID\tNAME\n")
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103 f.write(comp_str)
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104
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105 if params.biomassid:
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106 biomass_rxn = sbml_doc.getModel().getReaction(params.biomassid)
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107 else:
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108 biomass_rxn = get_biomass_rxn(sbml_doc)
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109 if not biomass_rxn:
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110 print("Warning: unable to retrieve biomass reaction")
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111 biomass_id = ""
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112 else:
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113 biomass_id = biomass_rxn.getId()
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114 print(f"Biomass reaction ID: {biomass_id}")
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115 if params.biomassid_outfile:
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116 with open(params.biomassid_outfile, "w") as f:
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117 f.write("#ID\n")
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118 f.write(f"{biomass_id}\n")
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119
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120 if params.taxonid:
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121 taxid = params.taxonid
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122 elif params.standalone:
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123 taxid = -1
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124 else:
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125 model_id = sbml_doc.getModel().getId()
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126 if model_id:
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127 taxid = get_taxon_id(sbml_doc.getModel().getId())
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128 if taxid == -1:
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129 # Try with model name
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130 model_name = sbml_doc.getModel().getName()
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131 if model_name:
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132 taxid = get_taxon_id(sbml_doc.getModel().getName())
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133 print(f"Taxonomy ID: {taxid}")
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134
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135 if params.taxonid_outfile:
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136 with open(params.taxonid_outfile, "w") as f:
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137 f.write("#ID\n")
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138 f.write(f"{taxid}\n")
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139
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140
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141 if __name__ == "__main__":
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142 entry_point()