From 88e6f64a73932b6907f626dbd42bc2beeff3fcca Mon Sep 17 00:00:00 2001
From: ChocolateCharlie <ChocolateCharlie@users.noreply.github.com>
Date: Wed, 29 Jun 2022 22:02:24 +0200
Subject: [PATCH] Clean hardcoded file names

---
 jupyter_notebooks/createModel.ipynb | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/jupyter_notebooks/createModel.ipynb b/jupyter_notebooks/createModel.ipynb
index 6ef050f7..e98e6c1b 100644
--- a/jupyter_notebooks/createModel.ipynb
+++ b/jupyter_notebooks/createModel.ipynb
@@ -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"
    ]
@@ -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')])"
    ]
   },
   {
@@ -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",
@@ -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",