comparison get_infos.py @ 12:1aadcfdae10b draft

planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 94f89a44e330ccfccc8d94b5e7acf583c9d39343

11:062f51695ae0

def args():
    parser = ArgumentParser("Returns cell informations")
    parser.add_argument("infile", type=str, help="SBML input file (xml)")
    parser.add_argument("--biomassid", type=str, help="ID of biomass reaction")
    parser.add_argument("--taxonid", type=str, help="Taxonomy ID")
    parser.add_argument("--standalone", action="store_true", help="Standalone mode, e.g. do not retrieve taxonomy ID on Internet (true if --taxonid is provided)")
    parser.add_argument("--compartments-outfile", type=str, help="Path to store cell compartments")
    parser.add_argument("--biomassid-outfile", type=str, help="Path to store biomass reaction ID")
    parser.add_argument("--taxonid-outfile", type=str, help="Path to store host taxonomy ID")
    params = parser.parse_args()
    return params


def get_organism_from_bigg_model(model_id):

    for comp in compartments:
        comp_str += f"{comp.getId()}\t{comp.getName()}\n"
    print("Compartments:")
    for comp in compartments:
        print(f"{comp.getId()}\t{comp.getName()}".replace("\n", " | "))
    if params.compartments_outfile:
        with open(params.compartments_outfile, "w") as f:
            f.write("#ID\tNAME\n")
            f.write(comp_str)

    if params.biomassid:
        biomass_rxn = sbml_doc.getModel().getReaction(params.biomassid)
    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()
    print(f"Biomass reaction ID: {biomass_id}")
    if params.biomassid_outfile:
        with open(params.biomassid_outfile, "w") as f:
            f.write("#ID\n")
            f.write(f"{biomass_id}\n")

    if params.taxonid:
        taxid = params.taxonid
    elif params.standalone:
        taxid = -1
    else:
        model_id = sbml_doc.getModel().getId()
        if model_id:
            taxid = get_taxon_id(sbml_doc.getModel().getId())
        if taxid == -1:
            # Try with model name
            model_name = sbml_doc.getModel().getName()
            if model_name:
                taxid = get_taxon_id(sbml_doc.getModel().getName())
    print(f"Taxonomy ID: {taxid}")

    if params.taxonid_outfile:
        with open(params.taxonid_outfile, "w") as f:
            f.write("#ID\n")
            f.write(f"{taxid}\n")


if __name__ == "__main__":

12:1aadcfdae10b

def args():
    parser = ArgumentParser("Returns cell informations")
    parser.add_argument("infile", type=str, help="SBML input file (xml)")
    parser.add_argument("--hostname-or-id", type=str, help="Hostname or model ID")
    parser.add_argument("--comp", type=str, help="Path to store cell compartments")
    parser.add_argument("--biomass", type=str, help="Path to store biomass reaction ID")
    parser.add_argument("--biomass-id", type=str, help="ID of biomass reaction")
    parser.add_argument("--taxid", type=str, help="Path to store host taxonomy ID")
    params = parser.parse_args()
    return params


def get_organism_from_bigg_model(model_id):

    for comp in compartments:
        comp_str += f"{comp.getId()}\t{comp.getName()}\n"
    print("Compartments:")
    for comp in compartments:
        print(f"{comp.getId()}\t{comp.getName()}".replace("\n", " | "))
    if params.comp:
        with open(params.comp, "w") as f:
            f.write("#ID\tNAME\n")
            f.write(comp_str)

    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()
    print(f"Biomass reaction ID: {biomass_id}")
    if params.biomass:
        with open(params.biomass, "w") as f:
            f.write("#ID\n")
            f.write(f"{biomass_id}\n")

    if params.hostname_or_id:
        taxid = get_taxon_id(params.hostname_or_id)
    else:
        model_id = sbml_doc.getModel().getId()
        taxid = -1
        if model_id:
            taxid = get_taxon_id(sbml_doc.getModel().getId())
        if taxid == -1:
            # Try with model name
            model_name = sbml_doc.getModel().getName()
            if model_name:
                taxid = get_taxon_id(sbml_doc.getModel().getName())
    print(f"Taxonomy ID: {taxid}")

    if params.taxid:
        with open(params.taxid, "w") as f:
            f.write("#ID\n")
            f.write(f"{taxid}\n")


if __name__ == "__main__":