#!/usr/bin/env python from __future__ import print_function from carveme import config, project_dir import argparse import os import pandas as pd from carveme.universe.bigg_download import build_bigg_universe_model, download_model_specific_data, create_gpr_table from carveme.universe.curation import curate_universe from carveme.universe.thermodynamics import compute_bigg_gibbs_energy from carveme.reconstruction.utils import load_biomass_db from framed.io.sbml import load_cbmodel def main(mode, noheuristics=False, nothermo=False, allow_unbalanced=False, allow_blocked=False, biomass=None, biomass_db_path=None, normalize_biomass=False, taxa=None, outputfile=None): if mode == 'draft': if outputfile: universe_draft = outputfile model_specific_data = os.path.splitext(outputfile)[0] + '.csv' bigg_gprs = os.path.splitext(outputfile)[0] + '_gprs.csv' else: universe_draft = project_dir + config.get('generated', 'universe_draft') model_specific_data = project_dir + config.get('generated', 'model_specific_data') bigg_gprs = project_dir + config.get('generated', 'bigg_gprs') build_bigg_universe_model(universe_draft) data = download_model_specific_data(model_specific_data) create_gpr_table(data, outputfile=bigg_gprs) elif mode == 'thermo': universe_draft = project_dir + config.get('generated', 'universe_draft') equilibrator_compounds = project_dir + config.get('input', 'equilibrator_compounds') if outputfile: bigg_gibbs = outputfile else: bigg_gibbs = project_dir + config.get('generated', 'bigg_gibbs') compute_bigg_gibbs_energy(universe_draft, equilibrator_compounds, bigg_gibbs) elif mode == 'curated': universe_draft = project_dir + config.get('generated', 'universe_draft') model_specific_data = project_dir + config.get('generated', 'model_specific_data') if not biomass: if taxa == 'archaea': biomass = 'archaea' else: biomass = config.get('universe', 'default_biomass') if outputfile: universe_final = outputfile else: tag = taxa if taxa != 'bacteria' else biomass universe_final = "{}{}universe_{}.xml.gz".format(project_dir, config.get('generated', 'folder'), tag) bigg_models = project_dir + config.get('input', 'bigg_models') bigg_models = pd.read_csv(bigg_models, index_col=0) manual_curation = project_dir + config.get('input', 'manually_curated') manually_curated = pd.read_csv(manual_curation, index_col=0) unbalanced = project_dir + config.get('input', 'unbalanced_metabolites') unbalanced = pd.read_csv(unbalanced, header=None) unbalanced = unbalanced[0].tolist() try: model = load_cbmodel(universe_draft, flavor=config.get('sbml', 'default_flavor')) model_specific_data = pd.read_csv(model_specific_data) except IOError: raise IOError('Universe draft not found. Please run --draft first to download BiGG data.') if biomass_db_path is None: biomass_db_path = project_dir + config.get('input', 'biomass_library') biomass_db = load_biomass_db(biomass_db_path, normalize_weight=normalize_biomass, model=model) if biomass not in biomass_db: valid_ids = ','.join(biomass_db.keys()) raise RuntimeError('Biomass identifier not in database. Currently in database: ' + valid_ids) biomass_eq = biomass_db[biomass] if nothermo: thermodynamics_data = None metabolomics_data = None else: try: bigg_gibbs = project_dir + config.get('generated', 'bigg_gibbs') thermodynamics_data = pd.read_csv(bigg_gibbs, index_col=0) except IOError: raise IOError('Thermodynamic data not found. Please run --thermo first to generate thermodynamic data.') metabolomics = project_dir + config.get('input', 'metabolomics') metabolomics_data = pd.read_csv(metabolomics, index_col=1) curate_universe(model, taxa=taxa, outputfile=universe_final, model_specific_data=model_specific_data, bigg_models=bigg_models, thermodynamics_data=thermodynamics_data, metabolomics_data=metabolomics_data, manually_curated=manually_curated, unbalanced_metabolites=unbalanced, biomass_eq=biomass_eq, use_heuristics=(not noheuristics), remove_unbalanced=(not allow_unbalanced), remove_blocked=(not allow_blocked)) else: print('Unrecognized option:', mode) if __name__ == '__main__': parser = argparse.ArgumentParser(description="Generate universal model to use with CarveMe") mode = parser.add_mutually_exclusive_group(required=True) mode.add_argument('--draft', action='store_true', help='Download all data from BiGG and save uncurated (draft) model to SBML.') mode.add_argument('--thermo', action='store_true', help='Compute thermodynamics data for BiGG reactions.') mode.add_argument('--curated', action='store_true', help='Generate curated universal model of bacterial metabolism.') parser.add_argument('-o', '--output', dest='output', help="Output file") parser.add_argument('--nothermo', action='store_true', help="Advanced options: do not use thermodynamics data") parser.add_argument('--noheuristics', action='store_true', help="Advanced options: do not apply heuristic reversibility rules") parser.add_argument('--unbalanced', action='store_true', help="Advanced options: allow unbalanced reactions") parser.add_argument('--blocked', action='store_true', help="Advanced options: allow blocked reactions") taxa = parser.add_mutually_exclusive_group(required=False) taxa.add_argument('--cyanobacteria', action='store_true', help='Generate a template for cyanobacteria (includes thylakoid compartment).') taxa.add_argument('--archaea', action='store_true', help='Generate a template for archaea (includes methanogenic reactions).') parser.add_argument('--biomass', help="Advanced options: biomass equation identifier") parser.add_argument('--biomass-db', dest='biomass_db', help="Advanced options: biomass database file") parser.add_argument('--normalize-biomass', dest='normalize_biomass', action='store_true', help="Advanced options: Normalize biomass dry weight to 1 gram") args = parser.parse_args() if args.nothermo and (args.draft or args.thermo): parser.error('--nothermo cannot be used with --draft or --thermo') if args.noheuristics and (args.draft or args.thermo): parser.error('--noheuristics cannot be used with --draft or --thermo') if args.unbalanced and (args.draft or args.thermo): parser.error('--unbalanced cannot be used with --draft or --thermo') if args.blocked and (args.draft or args.thermo): parser.error('--blocked cannot be used with --draft or --thermo') if args.biomass and (args.draft or args.thermo): parser.error('--biomass cannot be used with --draft or --thermo') if args.cyanobacteria and (args.draft or args.thermo): parser.error('--cyanobacteria cannot be used with --draft or --thermo') if args.archaea and (args.draft or args.thermo): parser.error('--archaea cannot be used with --draft or --thermo') if args.draft: mode = 'draft' elif args.thermo: mode = 'thermo' elif args.curated: mode = 'curated' if args.cyanobacteria: taxa = 'cyanobacteria' elif args.archaea: taxa = 'archaea' else: taxa = 'bacteria' main(mode=mode, nothermo=args.nothermo, noheuristics=args.noheuristics, allow_unbalanced=args.unbalanced, allow_blocked=args.blocked, biomass=args.biomass, biomass_db_path=args.biomass_db, normalize_biomass=args.normalize_biomass, taxa=taxa, outputfile=args.output)