| Previous changeset 7:8dc4d3964ab5 (2023-09-04) Next changeset 9:6a2871e89352 (2024-02-14) |
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Commit message:
planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit aa5a9ac47997d9c1718b9c7eaff1b83c63ac1d58 |
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modified:
get_infos.py get_sbml_model.xml |
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added:
model.sbml |
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| diff -r 8dc4d3964ab5 -r 768ed7cc0978 get_infos.py --- a/get_infos.py Mon Sep 04 14:19:43 2023 +0000 +++ b/get_infos.py Fri Sep 29 09:03:09 2023 +0000 |
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| @@ -5,7 +5,86 @@ from requests import get as r_get -def entry_point(): +def get_biomass_rxn(sbml_doc): + ''' + Returns the biomass reaction of the model + + Parameters + ---------- + sbml_doc: libsbml.SBMLDocument + SBML model + + Returns + ------- + biomass_rxn: libsbml.Reaction + Biomass reaction + ''' + reactions = sbml_doc.getModel().getListOfReactions() + # Search for 'biomass' keyword in reaction name + for rxn in reactions: + if 'biomass' in rxn.getName().lower(): + return rxn + # Search for 'biomass' keyword in products + # AND not in reactants + for rxn in reactions: + in_reactants = False + for reac in rxn.getListOfReactants(): + if 'biomass' in reac.getSpecies().lower(): + in_reactants = True + break + if not in_reactants: + for prod in rxn.getListOfProducts(): + if 'biomass' in prod.getSpecies().lower(): + return rxn + return None + + +def get_taxon_id(hostid): + ''' + Returns the taxonomy ID of the host organism + + Parameters + ---------- + hostid: str + Extended name of the host organism + + Returns + ------- + taxid: str + Taxonomy ID of the host organism + ''' + taxid = get_taxon_id(hostid) + hostname = '' + # Extended Name + server = 'http://bigg.ucsd.edu/api/v2/models/' + ext = hostid + r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) + if not r.ok: + print(f"Warning: unable to retrieve host name for id {hostid}") + else: + try: + hostname = r.json()["organism"] + except KeyError: + print(f"Warning: unable to retrieve host name for id {hostid}") + if not hostname: + taxid = '' + else: + # TAXON ID + server = 'https://rest.ensembl.org' + ext = f'/taxonomy/id/{hostname}?' + r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) + if not r.ok: + print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") + else: + try: + taxid = r.json()["id"] + except KeyError: + print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") + taxid = '' + return taxid + + +def args(): parser = ArgumentParser('Returns cell informations') parser.add_argument( 'infile', @@ -29,6 +108,11 @@ help='Path to store biomass reaction ID' ) parser.add_argument( + '--biomass-id', + type=str, + help='ID of biomass reaction' + ) + parser.add_argument( '--hostid', type=str, help='Extended name of the host organism' @@ -39,63 +123,57 @@ help='Path to store host taxonomy ID' ) params = parser.parse_args() + return params + + +def entry_point(): + + params = args() sbml_doc = readSBMLFromFile(params.infile) + compartments = sbml_doc.getModel().getListOfCompartments() + comp_str = '' + for comp in compartments: + comp_str += f'{comp.getId()}\t{comp.getName()}\n' if params.comp: - compartments = sbml_doc.getModel().getListOfCompartments() with open(params.comp, 'w') as f: f.write('#ID\tNAME\n') - for comp in compartments: - f.write(f'{comp.getId()}\t{comp.getName()}\n') + f.write(comp_str) + else: + print('Compartments:') + for comp in compartments: + print(f'{comp.getId()}\t{comp.getName()}'.replace('\n', ' | ')) + if params.biomass_id: + biomass_rxn = sbml_doc.getModel().getReaction(params.biomass_id) + else: + biomass_rxn = get_biomass_rxn(sbml_doc) + if not biomass_rxn: + print('Warning: unable to retrieve biomass reaction') + biomass_id = '' + else: + biomass_id = biomass_rxn.getId() if params.biomass: - reactions = sbml_doc.getModel().getListOfReactions() with open(params.biomass, 'w') as f: f.write('#ID\n') - for rxn in reactions: - if 'biomass' in rxn.getId().lower(): - f.write(f'{rxn.getId()}\n') + f.write(f'{biomass_id}\n') + else: + print(f'Biomass reaction ID: {biomass_id}') + + # Model from BiGG + if params.bigg: + taxid = get_taxon_id(params.hostid) + # Model from user + else: + taxid = params.hostid if params.taxid: - hostname = '' - - # Model from BiGG - if params.bigg: - # Extended Name - server = 'http://bigg.ucsd.edu/api/v2/models/' - ext = params.hostid - r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) - if not r.ok: - print(f"Warning: unable to retrieve host name for id {params.hostid}") - else: - try: - hostname = r.json()["organism"] - except KeyError: - print(f"Warning: unable to retrieve host name for id {params.hostid}") - if not hostname: - taxid = '' - else: - # TAXON ID - server = 'https://rest.ensembl.org' - ext = f'/taxonomy/id/{hostname}?' - r = r_get(server+ext, headers={ "Content-Type" : "application/json"}) - if not r.ok: - print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") - else: - try: - taxid = r.json()["id"] - except KeyError: - print(f"Warning: unable to retrieve taxonomy ID for host organism {hostname}") - taxid = '' - - # Model from user - else: - taxid = params.hostid - with open(params.taxid, 'w') as f: f.write('#ID\n') f.write(f'{taxid}\n') + else: + print(f'Taxonomy ID: {taxid}') if __name__ == "__main__": |
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| diff -r 8dc4d3964ab5 -r 768ed7cc0978 get_sbml_model.xml --- a/get_sbml_model.xml Mon Sep 04 14:19:43 2023 +0000 +++ b/get_sbml_model.xml Fri Sep 29 09:03:09 2023 +0000 |
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| @@ -20,6 +20,7 @@ python '$__tool_directory__/'get_infos.py #if str($cond_src.from_src) == 'from_bigg' '$model' + --bigg --taxid '$taxid' #else '${cond_src.input_file}' |
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| diff -r 8dc4d3964ab5 -r 768ed7cc0978 model.sbml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/model.sbml Fri Sep 29 09:03:09 2023 +0000 |
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| b'@@ -0,0 +1,169810 @@\n+<?xml version=\'1.0\' encoding=\'UTF-8\'?>\n+<sbml xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1" sboTerm="SBO:0000624" fbc:required="false">\n+ <model fbc:strict="true" id="iML1515">\n+ <listOfUnitDefinitions>\n+ <unitDefinition id="mmol_per_gDW_per_hr">\n+ <listOfUnits>\n+ <unit kind="mole" scale="-3" multiplier="1" exponent="1"/>\n+ <unit kind="gram" scale="0" multiplier="1" exponent="-1"/>\n+ <unit kind="second" scale="0" multiplier="3600" exponent="-1"/>\n+ </listOfUnits>\n+ </unitDefinition>\n+ </listOfUnitDefinitions>\n+ <fbc:listOfObjectives fbc:activeObjective="obj">\n+ <fbc:objective fbc:id="obj" fbc:type="maximize">\n+ <fbc:listOfFluxObjectives>\n+ <fbc:fluxObjective fbc:reaction="R_BIOMASS_Ec_iML1515_core_75p37M" fbc:coefficient="1"/>\n+ </fbc:listOfFluxObjectives>\n+ </fbc:objective>\n+ </fbc:listOfObjectives>\n+ <listOfParameters>\n+ <parameter value="-1000" id="cobra_default_lb" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>\n+ <parameter value="1000" id="cobra_default_ub" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>\n+ <parameter value="0" id="cobra_0_bound" sboTerm="SBO:0000626" constant="true" units="mmol_per_gDW_per_hr"/>\n+ <parameter id="R_EX_glc__D_e_lower_bound" value="-10" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>\n+ <parameter id="R_ATPM_lower_bound" value="6.86" sboTerm="SBO:0000625" constant="true" units="mmol_per_gDW_per_hr"/>\n+ </listOfParameters>\n+ <listOfCompartments>\n+ <compartment id="c" name="cytosol" constant="true"/>\n+ <compartment id="e" name="extracellular space" constant="true"/>\n+ <compartment id="p" name="periplasm" constant="true"/>\n+ </listOfCompartments>\n+ <listOfSpecies>\n+ <species id="M_octapb_c" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="Octanoate (protein bound)" metaid="M_octapb_c" sboTerm="SBO:0000247" compartment="c" fbc:charge="1" fbc:chemicalFormula="C8H15O">\n+ <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n+ <rdf:Description rdf:about="#M_octapb_c">\n+ <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/octapb"/>\n+ <rdf:li rdf:resource="http://identifiers.org/metanetx.chemical/MNXM147531"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </sbml:annotation>\n+ </species>\n+ <species id="M_cysi__L_e" constant="false" boundaryCondition="false" hasOnlySubstanceUnits="false" name="L Cystine C6H12N2O4S2" metaid="M_cysi__L_e" sboTerm="SBO:0000247" compartment="e" fbc:charge="0" fbc:chemicalFormula="C6H12N2O4S2">\n+ <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n+ <rdf:Description rdf:about="#M_cysi__L_e">\n+ <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.metabolite/cysi__L"/>\n+ <rdf:li rdf:resource="http://identifiers.org/biocyc/META:CYSTINE"/>\n+ <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:6209"/>\n+ <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:35491"/>\n+ <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:63163"/>\n+ <rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:13097"/>\n+ <rdf:li rdf:resource="htt'..b'istOfProducts>\n+ <speciesReference species="M_bmocogdp_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>\n+ </listOfProducts>\n+ <fbc:geneProductAssociation>\n+ <fbc:or>\n+ <fbc:and>\n+ <fbc:geneProductRef fbc:geneProduct="G_b3857"/>\n+ <fbc:geneProductRef fbc:geneProduct="G_b3856"/>\n+ </fbc:and>\n+ <fbc:geneProductRef fbc:geneProduct="G_b3857"/>\n+ </fbc:or>\n+ </fbc:geneProductAssociation>\n+ </reaction>\n+ <reaction id="R_FESD2s" fast="false" reversible="false" name="Iron-sulfur cluster damage (nitrous oxide, spontaneous)" metaid="R_FESD2s" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">\n+ <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n+ <rdf:Description rdf:about="#R_FESD2s">\n+ <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/FESD2s"/>\n+ <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR99586"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </sbml:annotation>\n+ <listOfReactants>\n+ <speciesReference species="M_4fe4s_c" stoichiometry="2" constant="true"/>\n+ <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>\n+ <speciesReference species="M_no_c" stoichiometry="2" constant="true"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference species="M_3fe4s_c" stoichiometry="2" constant="true"/>\n+ <speciesReference species="M_fe3_c" stoichiometry="2" constant="true"/>\n+ <speciesReference species="M_h2o_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_n2o_c" stoichiometry="1" constant="true"/>\n+ </listOfProducts>\n+ <fbc:geneProductAssociation>\n+ <fbc:geneProductRef fbc:geneProduct="G_s0001"/>\n+ </fbc:geneProductAssociation>\n+ </reaction>\n+ <reaction id="R_OCTNLL" fast="false" reversible="false" name="Octanoate non-lipoylated apo domain ligase" metaid="R_OCTNLL" sboTerm="SBO:0000176" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">\n+ <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">\n+ <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n+ <rdf:Description rdf:about="#R_OCTNLL">\n+ <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">\n+ <rdf:Bag>\n+ <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/OCTNLL"/>\n+ <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR102155"/>\n+ </rdf:Bag>\n+ </bqbiol:is>\n+ </rdf:Description>\n+ </rdf:RDF>\n+ </sbml:annotation>\n+ <listOfReactants>\n+ <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_octa_c" stoichiometry="1" constant="true"/>\n+ </listOfReactants>\n+ <listOfProducts>\n+ <speciesReference species="M_amp_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_octapb_c" stoichiometry="1" constant="true"/>\n+ <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>\n+ </listOfProducts>\n+ <fbc:geneProductAssociation>\n+ <fbc:geneProductRef fbc:geneProduct="G_b4386"/>\n+ </fbc:geneProductAssociation>\n+ </reaction>\n+ </listOfReactions>\n+ </model>\n+</sbml>\n' |