GapFillpy with results

Author: alejandrocs98

Proyecto-02/GapFill-GapFind/GapFind_GapFill.py

@@ -0,0 +1,51 @@
+# For using this module, you have to create a virtual environment.
+# Once created, you run the following command:
+# pip install git+https://github.com/zhanglab/psamm-import.git
+# 
+# Or you can follow this tutorial (useful for further information):
+# https://psamm.readthedocs.io/en/latest/index.html
+#
+# If attribute error due to fractions has no attribute "gcd", then modify the file
+# fractions.py importing gcd as follows:
+# from math import gcd
+#
+# Author: Sergio Pachón Dotor 
+# Github: https://github.com/SergioPachonDotor
+
+import os
+
+model_name = 'iAF1260_mutant_delta_f6p_c'
+model_path_sbml = f'./genome/Mutants/{model_name}.xml'
+model_path_yaml= f'./genome/{model_name}_yaml/'
+results_path= f'../../results/{model_name}/'
+
+def import_existing_model(ex_model_path=model_path_sbml, destination_path=model_path_yaml):
+    os.system(f'psamm-import sbml --source {ex_model_path} --dest {destination_path}')
+
+
+def gapfind_and_gapcheck(solver='gurobi', model_path=model_path_yaml, deep_check=False, results_path=results_path, file_name='gapcheck', file_extension='txt'):
+    
+    os.chdir(model_path)
+
+    if deep_check == True:
+        os.system(f'psamm-model gapcheck --method prodcheck --solver name={solver} > {results_path}{model_name}_{file_name}_prodcheck.{file_extension}', objective= 'thr__L_c')
+        os.system(f'psamm-model gapcheck --method sinkcheck --unrestricted-exchange --solver name={solver} > {results_path}{model_name}_{file_name}_sinkcheck_unrestricted-exchange.{file_extension}')
+        os.system(f'psamm-model gapcheck --method gapfind --unrestricted-exchange --solver name={solver} > {results_path}{model_name}_{file_name}_gapfind_unrestricted-exchange.{file_extension}')
+
+    if deep_check == False:
+        os.system(f'psamm-model gapcheck --method gapfind --unrestricted-exchange --solver name={solver} > {results_path}{model_name}_{file_name}_gapfind_unrestricted-exchange.{file_extension}')
+
+
+def gapfill_psamm(model_path=model_path_yaml, solver='gurobi', results_path=results_path, file_name='gapcheck', file_extension='txt'):
+    os.chdir(model_path)    
+    os.system(f'psamm-model gapfill --solver name={solver} --epsilon 0.0001 --compound thr__L_c > {results_path}{model_name}_{file_name}_gapfill.{file_extension}')
+
+def export_model():
+    pass
+
+
+if __name__ == '__main__':
+    # import_existing_model()
+    # gapfind_and_gapcheck()
+    # gapfill_psamm()
+    pass