def process_mdlr(self, mdlrPath):
'''
main method. extracts species definition, creates bng-xml, creates mdl
definitions
'''
try:
nauty_dict = self.xml2hnauty_species_definitions(mdlrPath)
except OSError:
print(
'Cannot open BNG2.pl. Please check BioNetGen is installed at: %s'
% (self.config['bionetgen']))
sys.exit(0)
# append extended bng-xml to the bng-xml definition (the one that
# doesn't include seed information)
bngxmlestr = writeBXe.merge_bxbxe(
namespace.input + '_rules.xml',
namespace.input + '_extended_bng.xml')
with open(mdlrPath + '_rules.xml', 'w') as f:
f.write(bngxmlestr)
xmlspec = read_bngxml.parseFullXML(namespace.input + '.xml')
# write out the equivalent plain mdl stuffs
mdl_dict = write_mdl.construct_mcell(xmlspec, namespace.input,
final_name.split(os.sep)[-1],
nauty_dict)
write_mdl.write_mdl(mdl_dict, final_name)
# temporaryly store bng-xml information in a separate file for display
# purposes
with open(namespace.input + '_extended.xml', 'wb') as f:
f.write(result_dict['bngxmlestr'])
# get cannonical label -bngl label dictionary
if not namespace.nfsim:
# bngl 2 sbml 2 json
read_mdl.bngl2json(namespace.input + '.bngl')
# json 2 plain mdl
mdl_dict = write_mdl.constructMDL(namespace.input + '_sbml.xml.json',
namespace.input, final_name)
# create an mdl with nfsim-species and nfsim-reactions
write_mdl.write_mdl(mdl_dict, final_name)
else:
try:
mdlr2mdl = MDLR2MDL(os.path.join(get_script_path(), 'mcellr.yaml'))
mdlr2mdl.process_mdlr(namespace.input)
except IOError:
print("Please create mcellr.yaml in the mcellRules directory. Use "
"mcellr.yaml.template as a reference.")
# get the species definitions
noext = os.path.splitext(namespace.input)[0]
xml_name = "{0}.mdlr_total.xml".format(noext)
mdl_name = "{0}.main.mdl".format(namespace.output)
with open("mcellr.yaml", 'r') as f:
config = yaml.load(f.read())
try:
mcell_path = config['mcell']