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Feat/new formats #88

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merged 8 commits into from
Apr 16, 2018
Merged

Feat/new formats #88

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6934645
refactor: saveYeastModel
BenjaSanchez Apr 12, 2018
406075a
feat: yaml file
BenjaSanchez Apr 12, 2018
7b72c7f
fix: rename folder
BenjaSanchez Apr 12, 2018
70fa5ea
doc: updated readme
BenjaSanchez Apr 12, 2018
1ae256c
fix: removed redundant pmid headers
BenjaSanchez Apr 12, 2018
7edff2d
Merge pull request #91 from SysBioChalmers/devel
BenjaSanchez Apr 13, 2018
0db74ca
chore: update yaml with changes from devel
BenjaSanchez Apr 13, 2018
c80e6ef
fix: ordered dictionary for compartments
BenjaSanchez Apr 13, 2018
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7 changes: 4 additions & 3 deletions ComplementaryScripts/saveYeastModel.m
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% saveYeastModel(model)
% Saves model as a .xml and .txt file. Also updates complementary files
% (boundaryMets.txt and dependencies.txt).
% Saves model as a .xml, .txt and .yml file. Also updates complementary
% files (boundaryMets.txt and dependencies.txt).
%
% Benjam�n J. S�nchez
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Expand All @@ -17,6 +17,7 @@ function saveYeastModel(model)
%Save changes to current model:
writeCbModel(model,'sbml','../ModelFiles/xml/yeastGEM.xml');
writeCbModel(model,'text','../ModelFiles/txt/yeastGEM.txt');
writeYaml(model,'../ModelFiles/yml/yeastGEM.yml');

%Detect boundary metabolites and save them in a .txt file:
fid = fopen('boundaryMets.txt','wt');
Expand All @@ -29,7 +30,7 @@ function saveYeastModel(model)
fclose(fid);

%Retrieve RAVEN version:
RAVENver = getVersion('checkInstallation.m','version.txt');
RAVENver = getVersion('ravenCobraWrapper.m','version.txt');

%Retrieve latest COBRA commit:
COBRApath = which('initCobraToolbox.m');
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