Mercurial > repos > tduigou > get_sbml_model

annotate get_infos.py @ 12:1aadcfdae10b draft

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planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343
author tduigou
date Tue, 01 Apr 2025 10:00:10 +0000
parents 062f51695ae0
children 6bcd8f09158d
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1 from argparse import ArgumentParser
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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()
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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:
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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("--hostname-or-id", type=str, help="Hostname or model ID")
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45 parser.add_argument("--comp", type=str, help="Path to store cell compartments")
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46 parser.add_argument("--biomass", type=str, help="Path to store biomass reaction ID")
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47 parser.add_argument("--biomass-id", type=str, help="ID of biomass reaction")
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48 parser.add_argument("--taxid", type=str, help="Path to store host taxonomy ID")
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49 params = parser.parse_args()
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50 return params
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52
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53 def get_organism_from_bigg_model(model_id):
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54 """Try to retrieve organism info from BiGG Models for a given model ID."""
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55 url = f"http://bigg.ucsd.edu/api/v2/models/{model_id}"
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56 try:
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57 response = r_get(url)
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58 if response.status_code == 200:
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59 data = response.json()
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60 organism = data.get("organism")
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61 return organism
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62 except Exception as e:
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63 print(f"Error querying BiGG: {e}")
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64 return None
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65
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66 def get_taxon_id(input_name):
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67 """Try BiGG model name first, then NCBI directly."""
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68 print(f"Trying input: {input_name}")
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69
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70 # Try resolving as a BiGG model
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71 organism = get_organism_from_bigg_model(input_name)
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72 if organism:
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73 print(f"Model '{input_name}' maps to organism: {organism}")
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74 taxon_id = get_taxonid(organism)
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75 if taxon_id:
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76 return taxon_id
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77
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78 # If not a model, try directly as an organism name
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79 print(f"Trying NCBI search with input: {input_name}")
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80 return get_taxonid(input_name)
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82
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83 def entry_point():
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84 params = args()
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85
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86 # test if the file exists
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87 with open(params.infile):
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88 pass
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89
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90 sbml_doc = readSBMLFromFile(params.infile)
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91
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92 compartments = sbml_doc.getModel().getListOfCompartments()
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93 comp_str = ""
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94 for comp in compartments:
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95 comp_str += f"{comp.getId()}\t{comp.getName()}\n"
dc1167469d62 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343
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96 print("Compartments:")
dc1167469d62 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343
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97 for comp in compartments:
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98 print(f"{comp.getId()}\t{comp.getName()}".replace("\n", " | "))
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99 if params.comp:
1aadcfdae10b planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343
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100 with open(params.comp, "w") as f:
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101 f.write("#ID\tNAME\n")
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102 f.write(comp_str)
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103
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104 if params.biomass_id:
1aadcfdae10b planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343
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105 biomass_rxn = sbml_doc.getModel().getReaction(params.biomass_id)
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768ed7cc0978 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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106 else:
768ed7cc0978 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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107 biomass_rxn = get_biomass_rxn(sbml_doc)
768ed7cc0978 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58
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108 if not biomass_rxn:
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109 print("Warning: unable to retrieve biomass reaction")
dc1167469d62 planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343
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110 biomass_id = ""
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111 else:
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112 biomass_id = biomass_rxn.getId()
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113 print(f"Biomass reaction ID: {biomass_id}")
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114 if params.biomass:
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115 with open(params.biomass, "w") as f:
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116 f.write("#ID\n")
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117 f.write(f"{biomass_id}\n")
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118
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119 if params.hostname_or_id:
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120 taxid = get_taxon_id(params.hostname_or_id)
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121 else:
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122 model_id = sbml_doc.getModel().getId()
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123 taxid = -1
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124 if model_id:
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125 taxid = get_taxon_id(sbml_doc.getModel().getId())
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126 if taxid == -1:
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127 # Try with model name
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128 model_name = sbml_doc.getModel().getName()
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129 if model_name:
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130 taxid = get_taxon_id(sbml_doc.getModel().getName())
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131 print(f"Taxonomy ID: {taxid}")
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132
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133 if params.taxid:
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134 with open(params.taxid, "w") as f:
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135 f.write("#ID\n")
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136 f.write(f"{taxid}\n")
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137
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138
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139 if __name__ == "__main__":
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140 entry_point()