def enumeration(sbml_folder, target_file, seed_file, output_json, host_file):
"""Run miscoto enumeration on one target file
Args:
sbml_folder (str): sbml directory
target_file (str): targets file
seed_file (str): seeds file
output_json (str): path to json output
host_file (str): metabolic network file for host
Returns:
str: path to output json
"""
results = miscoto.run_mincom(option="soup",
bacteria_dir=sbml_folder,
targets_file=target_file,
seeds_file=seed_file,
host_file=host_file,
intersection=True,
enumeration=True,
union=True,
optsol=True,
output_json=output_json)
# Give union of solutions
union = results['union_bacteria']
logger.info(
'######### Keystone species: Union of minimal communities #########')
logger.info(
"# Bacteria occurring in at least one minimal community enabling the producibility of the target metabolites given as inputs"
)
logger.info("Keystone species = " + str(len(union)))
logger.info("\n".join(union))
# Give intersection of solutions
intersection = results['inter_bacteria']
logger.info(
'######### Essential symbionts: Intersection of minimal communities #########'
)
logger.info(
"# Bacteria occurring in ALL minimal community enabling the producibility of the target metabolites given as inputs"
)
logger.info("Essential symbionts = " + str(len(intersection)))
logger.info("\n".join(intersection))
# Give keystones, essential and alternative symbionts
alternative_symbionts = list(set(union) - set(intersection))
logger.info(
'######### Alternative symbionts: Difference between Union and Intersection #########'
)
logger.info(
"# Bacteria occurring in at least one minimal community but not all minimal community enabling the producibility of the target metabolites given as inputs"
)
logger.info("Alternative symbionts = " + str(len(alternative_symbionts)))
logger.info("\n".join(alternative_symbionts))
return output_json
def compute_mincom(instancefile, output_dir):
"""Run minimal community selection and analysis.
Args:
instancefile (str): filepath to instance file
output_dir (str): directory with results
Returns:
dict: results of miscoto_mincom analysis
"""
miscoto_dir = output_dir + "/community_analysis"
if not utils.is_valid_dir(miscoto_dir):
logger.critical("Impossible to access/create output directory")
sys.exit(1)
results_dic = run_mincom(option="soup",
lp_instance_file=instancefile,
optsol=True,
union=True,
intersection=True)
return results_dic