upload helper scripts

code/04_gf_rxns_compile.sh

@@ -0,0 +1,5 @@
+while read model;do 
+	media=$(basename $(dirname $model));
+	species=$(basename ${model%.*});
+	less $model|grep GAP_FILL -B 12|grep "reaction id"|sed 's/ fast.*$//g'|sed 's/^.*<//g'|sed 's/reaction id="//g'|sed 's/ name="//g'|sed 's/ reversible="//g'|sed 's/"$//g'|tr '"' '\t'|sed "s/^/$media\t$species\t/g";
+done< <(find models/ -name "*.xml")

code/04_model_summary_compile.sh

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+while read file;do 
+ 	media=$(basename $(dirname $file));
+ 	model=$(basename $file|sed 's/.xml_summary.txt//g');
+ 	paste $file|grep -v Reactions|grep -v Metabolites|sed 's/ /\t/g'|sed "s/^/${model}\t${media}\t/g";
+done< <(find models/ -name "*summary.txt") > model_summary.tsv

code/04_model_summary_generate.py

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+import sys
+import glob
+import cobra
+import reframed
+from reframed import load_cbmodel
+from reframed import Environment
+from reframed import FBA
+
+# Loop to read in models in hardcoded folder with .xml extension
+for file in glob.iglob(r'*.xml'):
+
+	# Use try to handle exceptions with reading SMBL model
+	try:
+
+		# Load model
+		model = load_cbmodel(file, flavor='fbc2')
+
+		# open file
+		sys.stdout = open(file+"_summary.txt", "w")
+
+		# get summary
+		summary = model.summary()
+
+
+	# Catch cobra.io.sbml.CobraSBMLError and continue loop    
+	except cobra.io.sbml.CobraSBMLError:
+
+		# Print message with model ID for log
+		print("The model",file,"raised an SBML error and could not be read in by COBRA")
+		pass