From f774af4ff9b85d5d7f2cee4d9193f424e34c6044 Mon Sep 17 00:00:00 2001
From: Eduard Kerkhoven <eduardk@chalmers.se>
Date: Mon, 25 Nov 2024 00:31:15 +0100
Subject: [PATCH] fix: anaerobic_flux_predictions readtable

---
 code/modelTests/anaerobic_flux_predictions.m | 2 +-
 code/modelTests/anaerobiosis.m               | 4 ++--
 code/modelTests/growth.m                     | 6 ++----
 code/otherChanges/anaerobicModel.m           | 4 ++--
 4 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/code/modelTests/anaerobic_flux_predictions.m b/code/modelTests/anaerobic_flux_predictions.m
index 312da434..09ae9d6c 100644
--- a/code/modelTests/anaerobic_flux_predictions.m
+++ b/code/modelTests/anaerobic_flux_predictions.m
@@ -1,6 +1,6 @@
 function R2=anaerobic_flux_predictions(model)
 
-fluxTable=  readtable('../../data/physiology/flux_data_anaerobic.tsv');
+fluxTable = readtable('../../data/physiology/flux_data_anaerobic.tsv','FileType','text');
 fluxTable = table2cell(fluxTable);
 vals_flux=fluxTable;
 text_flux=fluxTable;
diff --git a/code/modelTests/anaerobiosis.m b/code/modelTests/anaerobiosis.m
index ec9d1b83..56ff442e 100644
--- a/code/modelTests/anaerobiosis.m
+++ b/code/modelTests/anaerobiosis.m
@@ -1,5 +1,6 @@
 clear; close all
 % Load the model and apply the corrections for *all* models
+model = readYAMLmodel('../../model/yeast-GEM.yml');
 cd('../modelCuration/')
 v9_1_0;
 
@@ -9,10 +10,9 @@
 %% Run growth tests
 R2 = growth(model);
 
-NLIM=0;
 %% Convert to anaerobic
 cd('../otherChanges/')
-model = anaerobicModel(model,0);
+model = anaerobicModel(model);
 
 cd('../modelTests/');
 %% flux predictions
diff --git a/code/modelTests/growth.m b/code/modelTests/growth.m
index 0aa80348..a8bc0fda 100644
--- a/code/modelTests/growth.m
+++ b/code/modelTests/growth.m
@@ -89,13 +89,11 @@
     model_origin = scaleBioMass(model_origin,'protein',0.289,'',false);
     model_origin = scaleBioMass(model_origin,'lipid',0.048,'',false);
     model_origin = scaleBioMass(model_origin,'RNA',0.077,'carbohydrate',false);
-    NLIM=1;
-else
-    NLIM=0;
+
 end
 
 if mode1 == 2
-    model_origin = anaerobicModel(model_origin,NLIM);
+    model_origin = anaerobicModel(model_origin);
 end
 for i = 1:length(exp_data(:,1))
     model_test= model_origin;
diff --git a/code/otherChanges/anaerobicModel.m b/code/otherChanges/anaerobicModel.m
index 80155359..fff9b6c0 100644
--- a/code/otherChanges/anaerobicModel.m
+++ b/code/otherChanges/anaerobicModel.m
@@ -9,7 +9,7 @@
 %   This function was updated as part of release v9.1.0.
 %
 % Input:
-%   model           model structure, which is aerobic by default
+%   model           yeast-GEM model structure, which is aerobic by default
 %
 % Output:
 %   model           model structure, modified to match anaerobic conditions
@@ -69,7 +69,7 @@
 % (2023) 10.1016/j.ymben.2024.01.007).
 model = setParam(model,'eq',{'r_0659'},0);
 
-%% Fumarate reductase is required for to recycle FADH2 dereived from
+%% Fumarate reductase is required for to recycle FADH2 derived from
 % disulphide bound formation in anaerobic conditions through Ero1 (Camarasa
 % et al (2007) 10.1002/yea.1467; Kim et al (2018) 10.1038/s41467-018-07285-9).