def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = '"End of code generated by Import Combine as PhrasedML plugin ' + time.strftime(
"%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(os.path.join(zipextloc, sbmlloclist[i]))
try:
transtext = te.sbmlToAntimony(sbml)
except Exception as e:
transtext = """*********************WARNING*********************
Failed to translate the SBML model to Antimony string.
Please check that the SBML file is valid.
*********************WARNING*********************"""
transtext = transtext + "\n\n" + str(e)
sbmlstrlist.append(transtext)
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(os.path.join(zipextloc, sedmlloclist[j]))
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(
"AntimonyModel = '''\n" + sbmlstrlist[0] +
"'''\n\nPhrasedMLstr = '''\n" + sedmlstrlist[k] +
"'''\n\nimport tellurium as te\n\nexp = te.experiment([AntimonyModel], [PhrasedMLstr])\nexp.execute(PhrasedMLstr)\n\n"
+ outputstr)
delseq(zipextloc)
return outputstrlist
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine with PhrasedML plugin ' + time.strftime(
"%m/%d/%Y"
) + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(zipextloc + sedmlloclist[j])
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + "AntimonyModel = '''\n" +
sbmlstrlist[0] +
"'''\n\nPhrasedMLstr = '''\n" +
sedmlstrlist[k] + "'''")
delseq(zipextloc)
return outputstrlist
def load_and_translate(self, sbmlfile, pythonfile, editor, set_current=True):
"""
Read filename as combine archive, unzip, translate, reconstitute in
Python, and create an editor instance and return it
*Warning* This is loading file, creating editor but not executing
the source code analysis -- the analysis must be done by the editor
plugin (in case multiple editorstack instances are handled)
"""
sbmlfile = str(sbmlfile)
self.emit(SIGNAL('starting_long_process(QString)'),
_("Loading %s...") % sbmlfile)
text, enc = encoding.read(sbmlfile)
sbmlstr = te.readFromFile(sbmlfile)
text = "import tellurium as te\n\nr = te.loada('''\n" + str(te.sbmlToAntimony(sbmlstr)) + "''')"
widgeteditor = editor.editorstacks[0]
finfo = widgeteditor.create_new_editor(pythonfile, enc, text, set_current, new=True)
index = widgeteditor.data.index(finfo)
widgeteditor._refresh_outlineexplorer(index, update=True)
self.emit(SIGNAL('ending_long_process(QString)'), "")
if widgeteditor.isVisible() and widgeteditor.checkeolchars_enabled \
and sourcecode.has_mixed_eol_chars(text):
name = os.path.basename(pythonfile)
QMessageBox.warning(self, widgeteditor.title,
_("<b>%s</b> contains mixed end-of-line "
"characters.<br>Spyder will fix this "
"automatically.") % name,
QMessageBox.Ok)
widgeteditor.set_os_eol_chars(index)
widgeteditor.is_analysis_done = False
finfo.editor.set_cursor_position('eof')
finfo.editor.insert_text(os.linesep)
return finfo, sbmlfile
def getODEsFromSBMLFile(fileName):
""" Given a SBML file name, this function returns the model
as a string of rules and ODEs
Args:
fileName (string): The path and name of the SBML file
Example:
>>> print (te.getODEsFromSBMLFile ('mymodel.xml'))
"""
sbmlStr = _te.readFromFile(fileName)
extractor = _ODEExtractor(sbmlStr)
return extractor._toString()
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"loadSBMLModel\((.*)\)"
reFig = r"savefig\((.*)\)"
outputstr = '"End of code generated by Import Combine plugin ' + time.strftime(
"%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(os.path.join(zipextloc, sbmlloclist[i]))
try:
transtext = te.sbmlToAntimony(sbml)
except Exception as e:
transtext = """*********************WARNING*********************
Failed to translate the SBML model to Antimony string.
Please check that the SBML file is valid.
*********************WARNING*********************"""
transtext = transtext + "\n\n" + str(e)
sbmlstrlist.append(transtext)
for j in range(len(sedmlloclist)):
sedmlstr = te.sedmlToPython(
os.path.join(zipextloc, sedmlloclist[j]))
lines = sedmlstr.splitlines()
for i, s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
s = s.replace("loadSBMLModel", "loada")
s = s.replace(reSearchPath[1], "AntimonyModel")
lines[i] = s
lines.insert(
i - 1,
"AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n")
for i, s in enumerate(lines):
reSearchFig = re.split(reFig, s)
if len(reSearchFig) > 1:
del lines[i]
sedmlstr = '\n'.join(lines)
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(sedmlstrlist[k] + '\n\n' + outputstr)
delseq(zipextloc)
return outputstrlist
def combineMotifs():
#Summary of motifs included
numReads = len(motifList)
print('-------------------------------')
print('There are ' + str(numReads) + ' motifs.')
#print(motifCopiedNum) ###See above TODO
print('-------------------------------')
#Label all models with an Alphabetically ordered key
reads = collections.OrderedDict({})
for i, ascii in zip(list(range(numReads)),
product_gen(string.ascii_uppercase)):
reads[ascii] = te.readFromFile(motifList[i])
### Initialize
models = list([reads.values()[0]])
species = []
currStr = reads.values()[0]
splitStr = re.split('(model)( [\*]?)(.*?\(*\))*\\n\\n', currStr)
modules = list([reads.keys()[0] + " : " + splitStr[3] + "; \n"])
modelList = list([splitStr[3]])
inputs = []
outputs = []
### Construct the combined model Antimony Code
for i in np.arange(1, numReads):
currStr = reads.values()[i]
splitStr = re.split('(model)( [\*]?)(.*?\(*\))*\\n\\n', currStr)
if splitStr[3] not in modelList:
models.append(reads.values()[i])
modelList.append(splitStr[3])
#Note: the modules have to call the model name within the .txt file for each motif, not the name of the .txt file
modules.append(reads.keys()[i] + " : " + splitStr[3] + "; \n") #i
species.append("var species p_c" + str(i) + "; \n") #i
inputs.append(reads.keys()[i - 1] + ".p_i" + " is p_c" + str(i) +
"; \n") #i-1
outputs.append(reads.keys()[i] + ".p_o" + " is p_c" + str(i) +
"; \n") #i
#combine lists to create a final 'combined' Antimony model
combined = "".join("".join(models) + 'model combined()\n' +
"".join(modules) + "".join(species) + "".join(inputs) +
"".join(outputs) + 'end')
return (combined)
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine with PhrasedML plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(zipextloc + sedmlloclist[j])
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + "AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n\nPhrasedMLstr = '''\n" + sedmlstrlist[k] + "'''")
delseq(zipextloc)
return outputstrlist
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
outputstr = '"End of code generated by Import Combine as PhrasedML plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = pl.convertFile(zipextloc + sedmlloclist[j])
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append("AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n\nPhrasedMLstr = '''\n" + sedmlstrlist[k] +
"'''\n\nimport tellurium as te\n\nexp = te.experiment([AntimonyModel], [PhrasedMLstr])\nexp.execute(PhrasedMLstr)\n\n" + outputstr)
delseq(zipextloc)
return outputstrlist
def translate(combine, filename):
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"loadSBMLModel\((.*)\)"
reFig = r"savefig\((.*)\)"
outputstr = '"End of code generated by Import Combine plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = te.sedmlToPython(zipextloc + sedmlloclist[j])
lines = sedmlstr.splitlines()
for i,s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
s = s.replace("loadSBMLModel", "loada")
s = s.replace(reSearchPath[1],"AntimonyModel")
lines[i] = s
lines.insert(i - 1, "AntimonyModel = '''\n" + sbmlstrlist[0] + "'''\n")
for i,s in enumerate(lines):
reSearchFig = re.split(reFig, s)
if len(reSearchFig) > 1:
del lines[i]
sedmlstr = '\n'.join(lines)
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(sedmlstrlist[k] + '\n\n' + outputstr)
delseq(zipextloc)
return outputstrlist
def translate(combine, filename):
tempPath = [[]]
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"(\w*).load\('(.*)'\)"
reLoad = r"(\w*) = roadrunner.RoadRunner\(\)"
reSelections = r'(\w+)\.selections = \[(.*),?\]'
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine plugin ' + time.strftime(
"%m/%d/%Y"
) + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = se.sedml_to_python(zipextloc + sedmlloclist[j])
lines = sedmlstr.splitlines()
for i, s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
modpath = getbasename(reSearchPath[2])[:-4].replace(
'-', '_')
if modpath[0].isdigit() == True:
modpath = 'Model_' + modpath
tempPath.append([reSearchPath[1], modpath])
else:
tempPath.append([reSearchPath[1], modpath])
#if '.xml' in s:
del lines[i]
for i, s in enumerate(lines):
reSearchLoad = re.split(reLoad, s)
if len(reSearchLoad) > 1:
for k in range(len(tempPath) - 1):
if reSearchLoad[1] == tempPath[k + 1][0]:
s = s.replace(
"roadrunner.RoadRunner()",
"te.loada(" + str(tempPath[k + 1][1]) + ")")
lines[i] = s
#if '"compartment"' or "'compartment'" in sedmlstr:
# reSearchSelections = re.split(reSelections, s)
# if len(reSearchSelections) > 1:
# Vars = reSearchSelections[2].replace(' ','').split(',')
# Vars = [s.replace('"','') for s in Vars]
# for i in range(len(Vars)):
# if Vars[i] == "compartment":
# Vars[i] = "compartment_"
if not "import tellurium" in sedmlstr:
if "import roadrunner" in sedmlstr:
for i, s in enumerate(lines):
if "import roadrunner" in s:
del lines[i]
lines.insert(i, "import tellurium as te")
else:
pass
else:
outputstr = outputstr + "import tellurium as te\n\n"
sedmlstr = '\n'.join(lines)
# List of replacements
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + tempPath[1][1] + " = '''\n" +
sbmlstrlist[0] + "'''\n\n" + sedmlstrlist[k])
delseq(zipextloc)
return outputstrlist
def sbmlconv(zipextloc):
sbmlloc, sedmlloc = manifestsearch(zipextloc)
sbml = te.readFromFile(zipextloc + sbmlloc)
sbmlantimony = te.sbmlToAntimony(sbml)
return sbmlantimony
def sbmlconv(zipextloc): #sbml conversion into antimony str
sbmlloc, sedmlloc = manifestsearch(zipextloc)
sbml = te.readFromFile(zipextloc + sbmlloc)
sbmlantimony = te.sbmlToAntimony(sbml)
return sbmlantimony
linewidth=2.0,
lineStyle='-',
color='black',
alpha=0.8)
r.k1 = r.k1 + 0.2
# Turn the notices back on
te.noticesOn()
# #### File helpers for reading and writing
# In[3]:
# create tmp file
import tempfile
ftmp = tempfile.NamedTemporaryFile(suffix=".xml")
print(ftmp.name)
# load model
r = te.loada('S1 -> S2; k1*S1; k1 = 0.1; S1 = 10')
# save to file
te.saveToFile(ftmp.name, r.getMatlab())
# or easier via
r.exportToMatlab(ftmp.name)
# load file
sbmlstr = te.readFromFile(ftmp.name)
print(sbmlstr)
# In[4]:
import re
np.set_printoptions(linewidth=160)
def product_gen(n):
for r in itertools.count(1):
for i in itertools.product(n, repeat=r):
yield "".join(i)
#%% Test model: putting two models together
numReads = 2
reads = {}
#for i in np.arange(0,numReads):
reads[0] = te.readFromFile('FFL1_ant.txt')
reads[1] = te.readFromFile('FFL2_ant.txt')
#generalize later
#combine this with for loop below this later
# Note: The string object name has to match the model name
readsalpha = zip(string.ascii_uppercase[:numReads], reads.values())
models = reads[0]
species = ""
currStr = readsalpha[0][1]
splitStr = re.split('(model)( [\*]?)(.*?)\\n\\n', currStr)
modules = readsalpha[0][0] + " : " + splitStr[3] + "; \n"
inputs = ""
outputs = ""
for i in np.arange(1, numReads):
def translate(combine, filename):
tempPath = [[]]
sbmlstrlist = []
sedmlstrlist = []
outputstrlist = []
rePath = r"(\w*).load\('(.*)'\)"
reLoad = r"(\w*) = roadrunner.RoadRunner\(\)"
reSelections = r'(\w+)\.selections = \[(.*),?\]'
outputstr = "# -*- coding: utf-8 -*-\n\n" + '"Generated by Import Combine plugin ' + time.strftime("%m/%d/%Y") + '"\n"Extracted from ' + filename + '"\n\n# Translated SBML\n'
zipextloc, sbmlloclist, sedmlloclist = manifestsearch(combine)
for i in range(len(sbmlloclist)):
sbml = te.readFromFile(zipextloc + sbmlloclist[i])
sbmlstrlist.append(te.sbmlToAntimony(sbml))
for j in range(len(sedmlloclist)):
sedmlstr = se.sedml_to_python(zipextloc + sedmlloclist[j])
lines = sedmlstr.splitlines()
for i,s in enumerate(lines):
reSearchPath = re.split(rePath, s)
if len(reSearchPath) > 1:
modpath = getbasename(reSearchPath[2])[:-4].replace('-','_')
if modpath[0].isdigit() == True:
modpath = 'Model_' + modpath
tempPath.append([reSearchPath[1], modpath])
else:
tempPath.append([reSearchPath[1], modpath])
#if '.xml' in s:
del lines[i]
for i,s in enumerate(lines):
reSearchLoad = re.split(reLoad, s)
if len(reSearchLoad) > 1:
for k in range(len(tempPath) - 1):
if reSearchLoad[1] == tempPath[k + 1][0]:
s = s.replace("roadrunner.RoadRunner()", "te.loada(" + str(tempPath[k + 1][1])+ ")")
lines[i] = s
#if '"compartment"' or "'compartment'" in sedmlstr:
# reSearchSelections = re.split(reSelections, s)
# if len(reSearchSelections) > 1:
# Vars = reSearchSelections[2].replace(' ','').split(',')
# Vars = [s.replace('"','') for s in Vars]
# for i in range(len(Vars)):
# if Vars[i] == "compartment":
# Vars[i] = "compartment_"
if not "import tellurium" in sedmlstr:
if "import roadrunner" in sedmlstr:
for i,s in enumerate(lines):
if "import roadrunner" in s:
del lines[i]
lines.insert(i, "import tellurium as te")
else:
pass
else:
outputstr = outputstr + "import tellurium as te\n\n"
sedmlstr = '\n'.join(lines)
# List of replacements
sedmlstr = sedmlstr.replace('"compartment"', '"compartment_"')
sedmlstr = sedmlstr.replace("'compartment'", "'compartment_'")
sedmlstrlist.append(sedmlstr)
for k in range(len(sedmlstrlist)):
outputstrlist.append(outputstr + tempPath[1][1] + " = '''\n" + sbmlstrlist[0] + "'''\n\n" + sedmlstrlist[k])
delseq(zipextloc)
return outputstrlist
r.k1 = r.k1 + 0.2
# Turn the notices back on
te.noticesOn()
# #### File helpers for reading and writing
# In[3]:
# create tmp file
import tempfile
ftmp = tempfile.NamedTemporaryFile(suffix=".xml")
print(ftmp.name)
# load model
r = te.loada('S1 -> S2; k1*S1; k1 = 0.1; S1 = 10')
# save to file
te.saveToFile(ftmp.name, r.getMatlab())
# or easier via
r.exportToMatlab(ftmp.name)
# load file
sbmlstr = te.readFromFile(ftmp.name)
print(sbmlstr)
# In[4]:
