diff --git a/bin/createModel.py b/bin/createModel.py index e2182ae9..3c793e77 100755 --- a/bin/createModel.py +++ b/bin/createModel.py @@ -50,7 +50,7 @@ volumes = [] # Create/write compartments -compartment_sheet = np.array([np.array(line.strip().split("\t")) for line in open('Compartments.txt')]) +compartment_sheet = np.array([np.array(line.strip().split("\t")) for line in open('Compartments.txt')], dtype=object) #read in each line minus the header row for row in compartment_sheet[1:]: @@ -65,7 +65,7 @@ fileModel.write("\n") # Write species and assign compartments -species_sheet = np.array([np.array(line.strip().split("\t")) for line in open('Species.txt', encoding='latin-1')]) +species_sheet = np.array([np.array(line.strip().split("\t")) for line in open('Species.txt', encoding='latin-1')], dtype=object) species_compartments = [] for row in species_sheet[1:]: @@ -84,7 +84,7 @@ fileModel.write("\n\n # Reactions:\n") #reads in file from excel and gets rid of first row and column (they're data labels) -stoic_sheet = np.array([np.array(line.strip().split("\t")) for line in open('StoicMat.txt')]) +stoic_sheet = np.array([np.array(line.strip().split("\t")) for line in open('StoicMat.txt')], dtype=object) #gets first column minus blank space at the beginning stoic_columnnames = stoic_sheet[0] @@ -92,8 +92,8 @@ stoic_data = np.array([line[1:] for line in stoic_sheet[1:]]) -ratelaw_sheet = np.array([np.array(line.strip().split("\t")) for line in open('Ratelaws.txt')]) -ratelaw_data = np.array([line[1:] for line in ratelaw_sheet[1:]]) +ratelaw_sheet = np.array([np.array(line.strip().split("\t")) for line in open('Ratelaws.txt')], dtype=object) +ratelaw_data = np.array([line[1:] for line in ratelaw_sheet[1:]], dtype=object) paramnames = [] paramvals = [] diff --git a/bin/modules/RunSPARCED.py b/bin/modules/RunSPARCED.py index b6278fd4..97c9e168 100644 --- a/bin/modules/RunSPARCED.py +++ b/bin/modules/RunSPARCED.py @@ -22,7 +22,7 @@ def RunSPARCED(flagD,th,spdata,genedata,sbml_file,model): splist = list(model.getStateIds()) if len(spdata)==0: # if no initial condition values are supplied, use the input file information spdata0 = pd.read_csv('Species.txt',header=0,index_col=0,sep="\t") - spdata = np.float(spdata0.values[:,1]) + spdata = np.float64(spdata0.values[:,1]) # calculate genedata, GenePositionMatrix, AllGenesVec, kTCmaxs, kTCleak, kGin_1, kGac_1, kTCd, TARs0, tcnas, tcnrs, tck50as, tck50rs, spIDs = RunPrep(flagD,Vn,model)