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feat: prepHumanModelForftINIT with paths #422

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Nov 6, 2022
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feat: prepHumanModelForftINIT with paths #422

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93e302a
fix: prepHumanModelForftINIT now allows for specifying the paths to t…
johan-gson Oct 12, 2022
03c5b83
Update code/tINIT/prepHumanModelForftINIT.m
johan-gson Oct 21, 2022
b591169
Update code/tINIT/prepHumanModelForftINIT.m
johan-gson Oct 21, 2022
da4dd40
Update code/tINIT/prepHumanModelForftINIT.m
johan-gson Oct 21, 2022
81a2c7f
style: Added some comments
johan-gson Oct 21, 2022
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19 changes: 14 additions & 5 deletions code/tINIT/prepHumanModelForftINIT.m
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@@ -1,22 +1,31 @@
function prepDataHumanGEM = prepHumanModelForftINIT(model, convertGenes)
function prepDataHumanGEM = prepHumanModelForftINIT(model, convertGenes, essentialTasksFilePath, rxnsFilePath)
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% prepHumanModelForftINIT
% Generates a "standard" prepData structure from Human-GEM to be used in ftINIT.
% This function typically takes a couple of hours to run, so we recommend to only
% run this once and save the results to a .mat file.
%
% model Either Human-GEM or a GEM derived from Human-GEM,
% such as Mouse-GEM.
% convertGenes True if the genes should be converted to symbols
% ('CD8A' etc., and not ENSEMBL)
% essentialTasksFilePath Path to the metabolicTasks_Essential.txt
% file. This file can normally be found under
% HumanGEM/data/metabolicTasks/metabolicTasks_Essential.txt
% If using for example Mouse-GEM, supply another path.
% rxnsFilePath Path to the reactions.tsv
% file. This file can normally be found under
% HumanGEM/model/reactions.tsv
% If using for example Mouse-GEM, supply another path.
%
% Usage: prepDataHumanGEM = prepHumanModelForftINIT(convertGenes)
% Usage: prepDataHumanGEM = prepHumanModelForftINIT(model, convertGenes, essentialTasksFilePath, rxnsFilePath)
%




%load tasks
taskStruct = parseTaskList(which('metabolicTasks_Essential.txt'));
taskStruct = parseTaskList(essentialTasksFilePath);
%Spontaneous reactions:
rxns_tsv = importTsvFile(which('reactions.tsv'));
rxns_tsv = importTsvFile(rxnsFilePath);
spont = rxns_tsv.spontaneous;
spontRxnNames = rxns_tsv.rxns(spont == 1);%very few

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