def metacom_analysis(sbml_dir, out_dir, seeds, host_mn):
"""Run the metabolism community analysis part of m2m.
Args:
sbml_dir (str): sbml input directory
out_dir (str): results directory
seeds (str): seeds file
host_mn (str): metabolic network file for host
"""
# INDIVIDUAL SCOPES
union_targets_iscope = iscope(sbml_dir, seeds, out_dir)
# COMMUNITY SCOPE
instance_com, targets_cscope = cscope(sbml_dir, seeds, out_dir, host_mn)
# ADDED VALUE
newtargets = addedvalue(union_targets_iscope, targets_cscope, out_dir)
if len(newtargets) > 0:
sbml_management.create_species_sbml(
newtargets, out_dir + "/community_analysis/targets.sbml")
logger.info("Target file created with the addedvalue targets in: " +
out_dir + "/community_analysis/targets.sbml")
# Add these targets to the instance
logger.info("Setting these " + str(len(newtargets)) + " as targets")
instance_w_targets = add_targets_to_instance(instance_com, out_dir,
newtargets)
# MINCOM
mincom(instance_w_targets, out_dir)
# remove intermediate files
os.unlink(instance_com)
os.unlink(instance_w_targets)
else:
logger.info(
"No newly producible compounds, hence no community selection will be computed"
)
os.unlink(instance_com)
def main_added_value(sbmldir, seeds, outdir, host):
"""Run addedvalue command.
Args:
sbmldir (str): SBML file directory
seeds (str): SBML file for seeds
outdir (str): results directory
host (str): SBML file for host
"""
iscope_metabolites = main_iscope(sbmldir, seeds, outdir)
#logger.info(", ".join(iscope_metabolites))
cscope_metabolites = main_cscope(sbmldir, seeds, outdir, host)
newtargets = addedvalue(iscope_metabolites, cscope_metabolites, outdir)
if len(newtargets) > 0:
sbml_management.create_species_sbml(newtargets, outdir + "/community_analysis/targets.sbml")
logger.info("Target file created with the addedvalue targets in: " +
outdir + "/community_analysis/targets.sbml")
def main_seeds(metabolites_file, outdir):
"""Run seeds command.
Args:
metabolites_file (str): text file with metabolites IDs, one per line
outdir (str): Results directory
"""
outfile = outdir + "/seeds.sbml"
with open(metabolites_file, "r") as f:
rawdata = f.readlines()
metabolites_set = set()
for elem in rawdata:
metabolites_set.add(elem.strip("\n"))
for metabolite in metabolites_set:
assert re.match(
"^[A-Za-z0-9_-]*$", metabolite
) and not metabolite[0].isdigit(
), "Seed file is not in the correct format. Error with %s. Example of a correct ID is M_OXYGEN__45__MOLECULE_c. Rules = only numbers, letters or underscore in IDs, not starting with a number. One ID per line." %(metabolite)
sbml_management.create_species_sbml(metabolites_set, outfile)
logger.info("Seeds SBML file created in " + outfile)
def metacom_analysis(sbml_dir, out_dir, seeds, host_mn, targets_file):
"""Run the metabolism community analysis part of m2m.
Args:
sbml_dir (str): sbml input directory
out_dir (str): results directory
seeds (str): seeds file
host_mn (str): metabolic network file for host
targets_file (str): targets file
"""
# INDIVIDUAL SCOPES
union_targets_iscope = iscope(sbml_dir, seeds, out_dir)
# COMMUNITY SCOPE
instance_com, targets_cscope = cscope(sbml_dir, seeds, out_dir,
targets_file, host_mn)
# ADDED VALUE
addedvalue_targets = addedvalue(union_targets_iscope, targets_cscope,
out_dir)
# If user gives a target file, check if the targets are in the addevalue
if targets_file is not None:
user_targets = set(sbml_management.get_compounds(targets_file))
newtargets = user_targets
individually_producible_targets = user_targets.intersection(
union_targets_iscope)
if len(individually_producible_targets) > 0:
logger.info(
'\n The following ' +
str(len(individually_producible_targets)) +
" targets are individually reachable by at least one organism: \n"
)
logger.info("\n".join(individually_producible_targets))
commonly_producible_targets = user_targets.intersection(
addedvalue_targets)
if len(commonly_producible_targets) > 0:
logger.info(
'\n The following ' + str(len(commonly_producible_targets)) +
" targets are additionally reachable through putative cooperation events: \n"
)
logger.info("\n".join(commonly_producible_targets))
else:
logger.info(
"Cooperation events do not enable the producibility of additional targets"
)
else:
user_targets = None
newtargets = addedvalue_targets
if len(newtargets) > 0:
target_file_path = os.path.join(
*[out_dir, 'community_analysis', 'targets.sbml'])
if targets_file is not None:
logger.info(
"\nTarget file created with the targets provided by the user in: "
+ target_file_path)
else:
sbml_management.create_species_sbml(newtargets, target_file_path)
logger.info(
"\nTarget file created with the addedvalue targets in: " +
target_file_path)
sbml_management.create_species_sbml(newtargets, target_file_path)
# Add these targets to the instance
logger.info("Setting " + str(len(newtargets)) +
" compounds as targets \n")
# if len(newtargets) != len(addedvalue_targets):
# logger.info("\n".join(newtargets))
instance_w_targets = add_targets_to_instance(instance_com, out_dir,
newtargets)
# MINCOM
mincom(instance_w_targets, out_dir)
# remove intermediate files
os.unlink(instance_com)
os.unlink(instance_w_targets)
else:
logger.info(
"No newly producible compounds, hence no community selection will be computed"
)
os.unlink(instance_com)
# Create targets result file
targets_producibility(out_dir, union_targets_iscope, targets_cscope,
addedvalue_targets, user_targets)