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Numpy version fixes. Backwards compatible with version 1.22.0, minor … #36

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Numpy version fixes. Backwards compatible with version 1.22.0, minor … #36

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10 changes: 5 additions & 5 deletions bin/createModel.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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:]:
Expand All @@ -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:]:
Expand All @@ -84,16 +84,16 @@
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]
stoic_rownames = [line[0] for line in stoic_sheet[1:]]
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 = []
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2 changes: 1 addition & 1 deletion bin/modules/RunSPARCED.py
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Expand Up @@ -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)
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