annotate get_infos.py @ 4:1482291aaa5c draft

planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 4a0b08beb8cdf51ab295a1f5f8c586d6bbaf5586

from argparse import ArgumentParser
from libsbml import (
    readSBMLFromFile
)
from requests import get as r_get


def entry_point():
    parser = ArgumentParser('Returns cell informations')
    parser.add_argument(
        'infile',
        type=str,
        help='SBML input file (xml)'
    )
    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(
        '--hostid',
        type=str,
        help='Extended name of the host organism'
    )
    parser.add_argument(
        '--taxid',
        type=str,
        help='Path to store host taxonomy ID'
    )
    params = parser.parse_args()

    sbml_doc = readSBMLFromFile(params.infile)

    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')

    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')

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


if __name__ == "__main__":
    entry_point()