comparison get_infos.py @ 10:dc1167469d62 draft

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

9:6a2871e89352

from argparse import ArgumentParser
from libsbml import (
    readSBMLFromFile
)
from taxonid import get_taxonid


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 args():
    parser = ArgumentParser('Returns cell informations')
    parser.add_argument(
        'infile',
        type=str,
        help='SBML input file (xml)'
    )
    # argument to tag file from BiGG
    parser.add_argument(
        '--bigg',
        action='store_true',
        help='Tag file from BiGG'
    )
    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(
        '--hostname',
        type=str,
        help='Name of the host organism'
    )
    parser.add_argument(
        '--taxid',
        type=str,
        help='Path to store host taxonomy ID'
    )
    params = parser.parse_args()
    return params


def get_taxon_id(hostid: str, bigg: bool):
    '''
    Returns the taxonomy ID of the host organism
    
    Parameters
    ----------
    hostid: str
        Extended name of the host organism or host ID if from BiGG
    bigg: bool
        True if the model is from BiGG
        
    Returns
    -------
    taxid: str
        Taxonomy ID of the host organism
    '''
    if not bigg:
        return get_taxonid(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 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:
        with open(params.comp, 'w') as f:
            f.write('#ID\tNAME\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:
        with open(params.biomass, 'w') as f:
            f.write('#ID\n')
            f.write(f'{biomass_id}\n')
    else:
        print(f'Biomass reaction ID: {biomass_id}')

    taxid = get_taxon_id(params.hostname, params.bigg)

    if params.taxid:
        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__":
    entry_point()

10:dc1167469d62

from argparse import ArgumentParser
from libsbml import readSBMLFromFile
from taxonid import get_taxonid
from requests import get as r_get


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 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):
    """Try to retrieve organism info from BiGG Models for a given model ID."""
    url = f"http://bigg.ucsd.edu/api/v2/models/{model_id}"
    try:
        response = r_get(url)
        if response.status_code == 200:
            data = response.json()
            organism = data.get("organism")
            return organism
    except Exception as e:
        print(f"Error querying BiGG: {e}")
    return None

def get_taxon_id(input_name):
    """Try BiGG model name first, then NCBI directly."""
    print(f"Trying input: {input_name}")
    
    # Try resolving as a BiGG model
    organism = get_organism_from_bigg_model(input_name)
    if organism:
        print(f"Model '{input_name}' maps to organism: {organism}")
        taxon_id = get_taxonid(organism)
        if taxon_id:
            return taxon_id

    # If not a model, try directly as an organism name
    print(f"Trying NCBI search with input: {input_name}")
    return get_taxonid(input_name)


def entry_point():
    params = args()

    # test if the file exists
    with open(params.infile):
        pass

    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"
    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__":
    entry_point()