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Clean hardcoded file names #10

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Clean hardcoded file names #10

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13 changes: 7 additions & 6 deletions jupyter_notebooks/createModel.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,8 @@
"outputs": [],
"source": [
"# Antimony model name and information text\n",
"fileModel = open('SPARCED.txt','w') # file name\n",
"fileModelName = 'SPARCED.txt'\n",
"fileModel = open(fileModelName,'w') # file name\n",
"fileModel.write(\"# PanCancer Model by Birtwistle Lab \\n\") # some explanation\n",
"fileModel.write(\"model SPARCED()\\n\") # model name"
]
Expand Down Expand Up @@ -199,7 +200,7 @@
"outputs": [],
"source": [
"# Write species and assign compartments\n",
"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(fileSpecies, encoding='latin-1')])"
]
},
{
Expand Down Expand Up @@ -253,10 +254,10 @@
"fileModel.write(\"\\n\\n # Reactions:\\n\") # Antimony Reactions module title\n",
"\n",
"#reads in file from excel and gets rid of first row and column (they're data labels)\n",
"stoic_sheet = np.array([np.array(line.strip().split(\"\\t\")) for line in open('StoicMat.txt')])\n",
"stoic_sheet = np.array([np.array(line.strip().split(\"\\t\")) for line in open(fileStoic)])\n",
"\n",
"#creates associated ratelaw data list\n",
"ratelaw_sheet = np.array([np.array(line.strip().split(\"\\t\")) for line in open('Ratelaws.txt')])\n",
"ratelaw_sheet = np.array([np.array(line.strip().split(\"\\t\")) for line in open(fileRatelaws)])\n",
"ratelaw_data = np.array([line[1:] for line in ratelaw_sheet[1:]])\n",
"\n",
"#gets first column minus blank space at the beginning, adds to stoic data list\n",
Expand Down Expand Up @@ -501,13 +502,13 @@
"outputs": [],
"source": [
"# load model and convert to SBML\n",
"if loadFile(\"SPARCED.txt\") == 1:\n",
"if loadFile(fileModelName) == 1:\n",
" print(\"Success loading antimony file\")\n",
"else:\n",
" print(\"Failed to load antimony file\")\n",
" exit(1)\n",
"\n",
"if writeSBMLFile(\"SPARCED.xml\",\"SPARCED\") == 1:\n",
"if writeSBMLFile(sbml_file,\"SPARCED\") == 1:\n",
" print(\"Success converting antimony to SBML\")\n",
"else:\n",
" print(\"Failure converting antimony to SBML\")\n",
Expand Down