def clone_mets(subsystem):
link_edges = []
CLONE_LEVEL = subsystem.get_param('CLONE_LEVEL')
LINK_CLONES = subsystem.get_param('LINK_CLONES')
CLONE_LINK_ATTRS = subsystem.get_param('CLONE_LINK_ATTRS')
def clone_out(sid):
current = [0]
def clone_aux(s):
if s.major and s.id == sid:
current[0] += 1
s.id += '#' + str(current[0])
if LINK_CLONES:
link_edges.append(Edge(s.id,s.label_id,
dir="none",**CLONE_LINK_ATTRS))
for rxn in subsystem.reactions:
for r in rxn.reactants:
clone_aux(r)
for p in rxn.products:
clone_aux(p)
if current[0] > 0:
link_edges.append(Node(sid,label=sid))
counts = minors.count_species(subsystem)
for count in counts:
if count.count >= CLONE_LEVEL:
clone_out(count.sid)
return link_edges
def metdraw(filename,count_mets=None,met_file=None,show=False,
engine='fdp',output='svg',quiet=False,q='1',Ln='1000',
json=False,norun=False,status=False,dotcmd='dot',no_gpr=False,
defaults=defaults):
sbml_filename = filename
if filename.endswith('.xml'):
filename = filename[:-4]
dot_filename = filename + '.dot'
mets_filename = filename + '.mets'
gpr_filename = filename + '.gpr'
output_filename = filename + '.' + output
if not quiet:
print 'Loading model file', sbml_filename
if filename.endswith('.json'):
model = Model.build_model(*model_json.parse_json_file(file=sbml_filename))
else:
pieces = sbml.parse_sbml_file(file=sbml_filename)
model = Model.build_model(**pieces)
if not no_gpr:
gpr.write_gpr_file(gpr.Gpr(pieces['reactions']),gpr_filename)
if not quiet:
print 'GPR written to file', gpr_filename
model.name = filename
model.set_param(**defaults)
if count_mets:
if not quiet:
print 'Writing metabolite counts to file', filename+'.mets'
Minors.write_met_file(Minors.count_species(model),
filename=mets_filename,
json=json)
return
if met_file:
minors = Minors.read_met_file(filename=met_file)
if not quiet:
print len(minors), "minors loaded from file '{0}'".format(met_file)
else:
# find the minors in the model; for now, we create a temporary mets
# file that is deleted after loading the minors
temp_filename = mets_filename + '.TEMP'
Minors.write_met_file(Minors.count_species(model),filename=temp_filename)
minors = Minors.read_met_file(temp_filename)
os.remove(temp_filename)
if not quiet:
print len(minors), "minors found in model"
model.set_param(name="minors",value=minors)
if show:
model.display()
display_parameters(defaults)
if not quiet:
print 'Creating reaction layout'
g = layout.model_to_dot(model)
if not quiet:
print 'Creating DOT file', dot_filename
g.to_file(dot_filename)
# run graphviz
if not quiet:
print 'Preparing Graphviz call:'
cmdstr = '{dot} -q{q} -Ln{Ln} -K{engine} -T{fmt} -o {outfile} {file}'
cmd = cmdstr.format(dot=dotcmd,
q=q,Ln=Ln,
engine=engine,
fmt=output,
outfile=output_filename,
file=dot_filename)
if not quiet:
print ' ' + cmd
if not norun:
print 'Running Graphviz'
error = os.system(cmd)
if error:
print "Error running dot:", error
else:
print 'ok'
# clean up intermediate DOT file
os.remove(dot_filename)
