From 317bdc26b90c38ab1cac80d6090e91b637f14b97 Mon Sep 17 00:00:00 2001
From: GwennyGit <81755070+GwennyGit@users.noreply.github.com>
Date: Tue, 8 Nov 2022 14:54:24 +0100
Subject: [PATCH] Enhanced applicability of the `polish.py` module #36  #46

1. Changed parameters in `config.yaml`:
- Renamed parameter `polish_carveme` to `polish`
- Added parameter `BiGG_IDs`
2. Changed `main.py` according to 'new' parameters
---
 config.yaml | 5 +++--
 main.py     | 7 +++++--
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/config.yaml b/config.yaml
index 0dedf7cf..daae5e3a 100644
--- a/config.yaml
+++ b/config.yaml
@@ -21,8 +21,9 @@ kegg_path:  '../C_striatum_GEMs/models/Cstr_KC-Na-01.xml' # path where to save m
 sboterms: FALSE
 sbo_path: '../C_striatum_GEMs/models/Cstr_KC-Na-01.xml' # path where to save model with sbo terms
 
-### CarveMe polishing ###
-polish_carveme: FALSE
+### Model polishing ### If model has no BiGG IDs, set parameter BiGG_IDs to FALSE
+polish: FALSE
+BiGG_IDs: TRUE
 polish_path: '../C_striatum_GEMs/models/Cstr_KC-Na-01.xml' # path where to save the polished model
 
 ### Charge correction ###
diff --git a/main.py b/main.py
index 5e050eff..80130a0a 100644
--- a/main.py
+++ b/main.py
@@ -29,9 +29,12 @@ def main():
         model, errors = cobra.io.sbml.validate_sbml_model(config['sbo_path'])
         print(errors)
         
-    elif (config['polish_carveme']):
+    elif (config['polish']):
         model_libsbml = rg.load.load_model_libsbml(config['model'])
-        rg.polish.polish_carveme_bigg(model_libsbml, config['polish_path'], config['entrez_email'])
+        if config['BiGG_IDs']:
+           rg.polish.polish_carveme_bigg(model_libsbml, config['polish_path'], config['entrez_email'])
+        else:
+         rg.polish.polish_not_bigg(model_libsbml, config['polish_path'], config['entrez_email'])
         model, errors = cobra.io.sbml.validate_sbml_model(config['polish_path'])
         print(errors)