Merge pull request #245 from SysBioChalmers/feat/addMAMids

feat: add MA met ids to metabolites.tsv

code/modelCuration/README.md

@@ -1,6 +1,5 @@
 # Model curation scripts
 
-This directory contains curation-related scripts and functions used to make changes to the Human-GEM model. These model curation scripts help to improve transparency of changes made to the model when the number of changes is too large to view practically.
+This directory contains curation-related scripts and functions used to make changes to the Human-GEM repository. These curation scripts help to improve transparency of changes made to the model when the number of changes is too large to view practically.
 
-Note that all code in this directory is considered deprecated and will not be updated or maintained.
 

code/modelCuration/addMAMetIDs.m

@@ -0,0 +1,70 @@
+% this script is to add metabolite identifiers (#174) that will be used for Met Atlas web-portal.
+
+% load data
+metIDs = importTsvFile('metabolites.tsv');
+
+% get compartment id for non-HMR mets that will be used later
+compID = cellfun(@(x) regexprep(x, '^.+_(\w)$', '$1'), metIDs.mets, 'UniformOutput', false);
+matche2NonHMR = regexp(metIDs.mets, '_\w$', 'match');
+emptymask = cellfun('isempty', matche2NonHMR);
+compID(emptymask) = {''};    % empty HMR met ids
+
+% generate MA met ids from HMR ids only with "MA-" prefix
+metMAID = cellfun(@(x) regexprep(x, '^m(\d\d\d\d\d\w)$', 'MA-M$1'), metIDs.mets, 'UniformOutput', false);
+
+% check consistency between HMR ids and empty elemnets of non-HMR ids
+matche2HMR = regexp(metMAID, '^MA-M\d\d\d\d\d\w$', 'match');
+ind2HMR = ~cellfun('isempty', matche2HMR);
+check = find(ind2HMR ~= emptymask);
+metIDs.mets(check)
+%    {'temp001c'}
+%    {'temp001s'}
+% these two mets are from HMR but in non-standard format, will be treated as
+% non-HMR ids
+compID(check) = {'c';'s'};
+
+% kepp HMR ids in metMAID and clean others
+ind_MAID = startsWith(metMAID, 'MA-M');
+metMAID(~ind_MAID) = {''};
+metMAIDNoComp = cellfun(@(x) regexprep(x, '^(.+)\w$', '$1'), metMAID, 'UniformOutput', false);
+
+% get index of nonHMR ids from compID and remove their comppart id
+nonHMRidInd = ~cellfun('isempty', compID);
+nonHMRidNoComp = cellfun(@(x) regexprep(x, '^(.+)_\w$', '$1'), metIDs.mets(nonHMRidInd), 'UniformOutput', false);
+
+% get unique list of nonHMR ids
+[uniqueID, ia, ic] = unique(nonHMRidNoComp);
+%isequal(nonHMRidNoComp, uniqueID(ic))
+%isequal(uniqueID, nonHMRidNoComp(ia))
+
+% prepare standard format MA ids for nonHMR mets
+idsToAdd = cell(10000,1);
+for i=1:10000
+    idsToAdd{i} = strcat('MA-M',sprintf('%05d', i));
+end
+idsToAdd = setdiff(idsToAdd, metMAIDNoComp);     % exclude existing ones
+idsToAdd = idsToAdd(1:length(uniqueID));
+
+% get ids to fill in
+idsToFill = idsToAdd(ic);
+
+% append compartment id to idsToFill
+idsToFill = strcat(idsToFill,compID(nonHMRidInd));
+
+% complete MA met ids
+metMAID(nonHMRidInd) = idsToFill;
+
+% format check
+all(cell2mat(regexp(metMAID, '^MA-M\d\d\d\d\d\w$')))
+% unique check
+isequal(length(metMAID), length(sort(metMAID)))
+% empty check
+B = cellfun('isempty', metMAID);
+all(B(:) == 0)
+
+% add new field and output
+metIDs.metMAID = metMAID;
+exportTsvFile(metIDs,'metabolites.tsv');
+
+
+

code/modelCuration/completeMARxnids.m

@@ -0,0 +1,28 @@
+% this script is to provide complete reaction identifiers (#174) that will be used for Met Atlas web-portal.
+
+% load reaction ids
+rxnIDs = importTsvFile('reactions.tsv');
+
+% replace underscore with `R`
+rxnIDs.rxnMAID = strrep(rxnIDs.rxnMAID,'_','R');
+indToFill = getNonEmptyList(rxnIDs.rxnMAID,false);
+
+% prepare a list to fill
+idsToAdd = cell(19999,1);
+for i=1:19999
+    idsToAdd{i} = strcat('MAR',sprintf('%05d', i));
+end
+idsToAdd = setdiff(idsToAdd, rxnIDs.rxnMAID);
+
+% sequentially fill in blank MA ids
+rxnIDs.rxnMAID(indToFill) = idsToAdd(1:length(indToFill));
+if isequal(length(rxnIDs.rxnMAID), length(unique(rxnIDs.rxnMAID)))
+    fprintf('the filling looks okay.\n');
+end
+
+% insert dash between MA and RDDDDD
+rxnIDs.rxnMAID = strrep(rxnIDs.rxnMAID,'MA','MA-');
+
+
+exportTsvFile(rxnIDs,'reactions.tsv'); 
+