fix: rename model files to yeast-GEM

SysBioChalmers · Jun 24, 2021 · 919d396 · 919d396
1 parent c0113a1
commit 919d396
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Showing 15 changed files with 38 additions and 38 deletions.
diff --git a/.github/workflows/yaml-validation.yml b/.github/workflows/yaml-validation.yml
@@ -36,4 +36,4 @@ jobs:
     - name: Import with cobrapy
       run: |
         pip install -r requirements/ci-requirements.txt
-        python -c "import cobra ; cobra.io.load_yaml_model('model/yeastGEM.yml')"
+        python -c "import cobra ; cobra.io.load_yaml_model('model/yeast-GEM.yml')"
diff --git a/README.md b/README.md
@@ -36,7 +36,7 @@ This repository contains the current consensus genome-scale metabolic model of _
 |:-------:|:--------------:|:---------:|:----------:|:-----:|
 |_Saccharomyces cerevisiae_|[Yeast 7.6](https://sourceforge.net/projects/yeast/)|4058|2742|1150|
 
-**Last update:** 2021-06-15
+**Last update:** 2021-06-24
 
 ## Installation
 

diff --git a/code/deprecated/modelCuration/addiSce926changes.m b/code/deprecated/modelCuration/addiSce926changes.m
@@ -7,7 +7,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 %Load model:
-model = readCbModel('../../model/yeastGEM.xml');
+model = readCbModel('../../model/yeast-GEM.xml');
 
 %Correct some gene relations based on isce926:
 fid      = fopen('../../data/modelCuration/iSce926curatedGeneRules.tsv');

diff --git a/code/increaseVersion.m b/code/increaseVersion.m
@@ -20,7 +20,7 @@ function increaseVersion(bumpType)
 end
 
 %Bump version number:
-oldModel   = load('../model/yeastGEM.mat');
+oldModel   = load('../model/yeast-GEM.mat');
 oldVersion = oldModel.model.modelID;
 oldVersion = oldVersion(strfind(oldVersion,'_v')+2:end);
 oldVersion = str2double(strsplit(oldVersion,'.'));
@@ -50,21 +50,21 @@ function increaseVersion(bumpType)
 
 %Load model:
 initCobraToolbox
-model = readCbModel('../model/yeastGEM.xml');
+model = readCbModel('../model/yeast-GEM.xml');
 
 %Include tag and save model:
-model.modelID = ['yeastGEM_v' newVersion];
+model.modelID = ['yeast-GEM_v' newVersion];
 saveYeastModel(model,false,false)   %only save if model can grow
 
-%Check if any file changed (except for history.md and 1 line in yeastGEM.xml):
+%Check if any file changed (except for history.md and 1 line in yeast-GEM.xml):
 diff   = git('diff --numstat');
 diff   = strsplit(diff,'\n');
 change = false;
 for i = 1:length(diff)
     diff_i = strsplit(diff{i},'\t');
     if length(diff_i) == 3
         %.xml file: 1 line should be added & 1 line should be deleted
-        if strcmp(diff_i{3},'model/yeastGEM.xml')
+        if strcmp(diff_i{3},'model/yeast-GEM.xml')
             if eval([diff_i{1} ' > 1']) || eval([diff_i{2} ' > 1'])
                 disp(['NOTE: File ' diff_i{3} ' is changing more than expected'])
                 change = true;
@@ -98,7 +98,7 @@ function increaseVersion(bumpType)
 delete('backup');
 
 %Store model as .mat:
-save('../model/yeastGEM.mat','model');
+save('../model/yeast-GEM.mat','model');
 
 %Convert to RAVEN format and store model as .xlsx:
 model = ravenCobraWrapper(model);
@@ -110,7 +110,7 @@ function increaseVersion(bumpType)
 model.annotation.email        = '[email protected]';
 model.annotation.organization = 'Chalmers University of Technology';
 model.annotation.note         = 'Saccharomyces cerevisiae - strain S288C';
-exportToExcelFormat(model,'../model/yeastGEM.xlsx');
+exportToExcelFormat(model,'../model/yeast-GEM.xlsx');
 
 %Update version file:
 fid = fopen('../version.txt','wt');

diff --git a/code/io.py b/code/io.py
@@ -11,7 +11,7 @@
 # find .env + define paths:
 dotenv_path = find_dotenv()
 REPO_PATH = dirname(dotenv_path)
-MODEL_PATH = f"{REPO_PATH}/model/yeastGEM.xml"
+MODEL_PATH = f"{REPO_PATH}/model/yeast-GEM.xml"
 
 def read_yeast_model(make_bigg_compliant=False):
     """Reads the SBML file of the yeast model using COBRA.

diff --git a/code/loadYeastModel.m b/code/loadYeastModel.m
@@ -7,7 +7,7 @@
 
 scriptFolder = fileparts(which(mfilename));
 currentDir = cd(scriptFolder);
-model = readCbModel('../model/yeastGEM.xml');
+model = readCbModel('../model/yeast-GEM.xml');
 model = buildRxnGeneMat(model);
 cd(currentDir)
 

diff --git a/code/missingFields/BiGGidsCompliance.ipynb b/code/missingFields/BiGGidsCompliance.ipynb
@@ -125,7 +125,7 @@
     "\n",
     "# Create new BiGG ids compliant with lipid standards:\n",
     "import cobra\n",
-    "model = cobra.io.read_sbml_model(\"../../model/yeastGEM.xml\")\n",
+    "model = cobra.io.read_sbml_model(\"../../model/yeast-GEM.xml\")\n",
     "file_name = '../../data/databases/BiGGmetDictionary_newIDs.csv'\n",
     "new_file_name = file_name.replace(\".csv\",\"_new.csv\")\n",
     "with open(file_name) as old_file:\n",
@@ -196,7 +196,7 @@
    "source": [
     "# Create new BiGG ids for SLIME rxns compliant with lipid standards:\n",
     "import cobra\n",
-    "model = cobra.io.read_sbml_model(\"../../model/yeastGEM.xml\")\n",
+    "model = cobra.io.read_sbml_model(\"../../model/yeast-GEM.xml\")\n",
     "file_name = '../../data/databases/BiGGrxnDictionary_newIDs.csv'\n",
     "new_file_name = file_name.replace(\".csv\",\"_new.csv\")\n",
     "with open(file_name) as old_file:\n",
@@ -237,7 +237,7 @@
    "source": [
     "# Create new BiGG ids for exchange rxns:\n",
     "import cobra\n",
-    "model = cobra.io.read_sbml_model(\"../../model/yeastGEM.xml\")\n",
+    "model = cobra.io.read_sbml_model(\"../../model/yeast-GEM.xml\")\n",
     "file_name = '../../data/databases/BiGGrxnDictionary_newIDs.csv'\n",
     "new_file_name = file_name.replace(\".csv\",\"_new.csv\")\n",
     "with open(file_name) as old_file:\n",
@@ -291,7 +291,7 @@
     "\n",
     "# Create new BiGG ids for exchange rxns:\n",
     "import cobra\n",
-    "model = cobra.io.read_sbml_model(\"../../model/yeastGEM.xml\")\n",
+    "model = cobra.io.read_sbml_model(\"../../model/yeast-GEM.xml\")\n",
     "file_name = '../../data/databases/BiGGrxnDictionary_newIDs.csv'\n",
     "new_file_name = file_name.replace(\".csv\",\"_new.csv\")\n",
     "with open(file_name) as old_file:\n",
@@ -341,7 +341,7 @@
     "import csv\n",
     "from copy import copy\n",
     "from re import findall\n",
-    "model = cobra.io.read_sbml_model(\"../../model/yeastGEM.xml\")\n",
+    "model = cobra.io.read_sbml_model(\"../../model/yeast-GEM.xml\")\n",
     "file_name = '../../data/databases/BiGGrxnDictionary_newIDs.csv'\n",
     "new_file_name = file_name.replace(\".csv\",\"_new.csv\")\n",
     "with open(file_name) as old_file:\n",

diff --git a/code/missingFields/GetMNXID.m b/code/missingFields/GetMNXID.m
@@ -5,7 +5,7 @@
 %   HMR3, and the part 'Load MNXref data structure' is modified to read the reference data from RAVEN.
 %
 %   model                   a model structure;please load yeast model using function 'loadYeastModel.m' from
-%                           yeastGEM github repository.
+%                           yeast-GEM github repository.
 %   type                    type = 'mets' or 'rxns'
 %   level                   level = 1:only compares MNXid FROM kegg and CHEBI
 %                           level =2 compares MNX from yeast7.6MNX model and CHEBI and KEGG

diff --git a/code/modelTests/cobrapy-compliance.ipynb b/code/modelTests/cobrapy-compliance.ipynb
@@ -25,7 +25,7 @@
    ],
    "source": [
     "import cobra\n",
-    "model = cobra.io.read_sbml_model(\"../../model/yeastGEM.xml\")"
+    "model = cobra.io.read_sbml_model(\"../../model/yeast-GEM.xml\")"
    ]
   },
   {

diff --git a/code/saveYeastModel.m b/code/saveYeastModel.m
@@ -57,10 +57,10 @@ function saveYeastModel(model,upDATE,allowNoGrowth)
 checkGrowth(model,'anaerobic',allowNoGrowth)
 
 %Update .xml, .txt and .yml models:
-copyfile('tempModel.xml','../model/yeastGEM.xml')
+copyfile('tempModel.xml','../model/yeast-GEM.xml')
 delete('tempModel.xml');
-writeCbModel(model,'text','../model/yeastGEM.txt');
-exportForGit(model,'yeastGEM','../model',{'yml'},false,false);
+writeCbModel(model,'text','../model/yeast-GEM.txt');
+exportForGit(model,'yeast-GEM','../model',{'yml'},false,false);
 
 %Detect boundary metabolites and save them in a .txt file:
 fid = fopen('../model/boundaryMets.txt','wt');
@@ -100,9 +100,9 @@ function saveYeastModel(model,upDATE,allowNoGrowth)
 
 %Convert notation "e-005" to "e-05 " in stoich. coeffs. to avoid
 %inconsistencies between Windows and MAC:
-copyfile('../model/yeastGEM.xml','backup.xml')
+copyfile('../model/yeast-GEM.xml','backup.xml')
 fin  = fopen('backup.xml','r');
-fout = fopen('../model/yeastGEM.xml','w');
+fout = fopen('../model/yeast-GEM.xml','w');
 still_reading = true;
 while still_reading
     inline = fgets(fin);

diff --git a/data/databases/BiGGrxnDictionary_newIDs.csv b/data/databases/BiGGrxnDictionary_newIDs.csv
@@ -1697,7 +1697,7 @@ r_2080,TREtv
 r_2082,TRP__Ltm
 r_2087,TYR__Ltx
 r_2107,ZYMSTtce
-r_2108,BIOMASS_yeastGEM_LIP
+r_2108,BIOMASS_yeast-GEM_LIP
 r_2111,GROWTH
 r_2125,COAtlp
 r_2134,EX_44mzym_e
@@ -2191,11 +2191,11 @@ r_3996,PCHOL_CHOtrm
 r_4005,PE_HStrm
 r_4038,TAG_CHOtrm
 r_4040,HEMEAtm
-r_4041,BIOMASS_yeastGEM
-r_4047,BIOMASS_yeastGEM_PROT
-r_4048,BIOMASS_yeastGEM_CARB
-r_4049,BIOMASS_yeastGEM_RNA
-r_4050,BIOMASS_yeastGEM_DNA
+r_4041,BIOMASS_yeast-GEM
+r_4047,BIOMASS_yeast-GEM_PROT
+r_4048,BIOMASS_yeast-GEM_CARB
+r_4049,BIOMASS_yeast-GEM_RNA
+r_4050,BIOMASS_yeast-GEM_DNA
 r_4051,CERtg
 r_4052,MIP2Ctg
 r_4053,IPCtg
@@ -2208,9 +2208,9 @@ r_4059,LPItrm
 r_4060,PGtmm
 r_4061,CLtmm
 r_4062,SINK_LIPBACK
-r_4063,BIOMASS_yeastGEM_LIPBACK
+r_4063,BIOMASS_yeast-GEM_LIPBACK
 r_4064,SINK_LIPCHAIN
-r_4065,BIOMASS_yeastGEM_LIPCHAIN
+r_4065,BIOMASS_yeast-GEM_LIPCHAIN
 r_4066,cer1_24SLIMEg
 r_4067,cer1_26SLIMEg
 r_4068,cer2_24SLIMEg
@@ -2557,5 +2557,5 @@ r_4586,STASYN
 r_4587,CA2t3ec
 r_4589,CU2TRA
 r_4592,MGt2ec
-r_4598,BIOMASS_yeastGEM_COFACTOR
-r_4599,BIOMASS_yeastGEM_ION
+r_4598,BIOMASS_yeast-GEM_COFACTOR
+r_4599,BIOMASS_yeast-GEM_ION
diff --git a/model/dependencies.txt b/model/dependencies.txt
@@ -1,6 +1,6 @@
 MATLAB	9.10.0.1602886 (R2021a)
 libSBML	5.17.0
-RAVEN_toolbox	commit 3b821c2
+RAVEN_toolbox	2.5.1
 COBRA_toolbox	commit 25dbea4
 SBML_level	3
 SBML_version	1

diff --git a/model/yeastGEM.txt → model/yeast-GEM.txt b/model/yeastGEM.txt → model/yeast-GEM.txt
diff --git a/model/yeastGEM.xml → model/yeast-GEM.xml b/model/yeastGEM.xml → model/yeast-GEM.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" xmlns:fbc="http://www.sbml.org/sbml/level3/version1/fbc/version2" xmlns:groups="http://www.sbml.org/sbml/level3/version1/groups/version1" level="3" version="1" fbc:required="false" groups:required="false">
-  <model metaid="yeastGEM.xml" id="M_yeastGEM_devel" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
+  <model metaid="yeast-GEM.xml" id="M_yeast__45__GEM_devel" name="The Consensus Genome-Scale Metabolic Model of Yeast" fbc:strict="true">
     <listOfUnitDefinitions>
       <unitDefinition id="mmol_per_gDW_per_hr">
         <listOfUnits>

diff --git a/model/yeastGEM.yml → model/yeast-GEM.yml b/model/yeastGEM.yml → model/yeast-GEM.yml
@@ -1,9 +1,9 @@
 ---
 !!omap
 - metaData:
-    id: "yeastGEM_devel"
+    id: "yeast-GEM_devel"
     name: "The Consensus Genome-Scale Metabolic Model of Yeast"
-    date: "2021-06-15"
+    date: "2021-06-24"
 - metabolites:
     - !!omap
       - id: "s_0001"