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fix: read EC numbers joined by a semicolon without a space as separate codes #14

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Merged
edkerk merged 1 commit into from
Oct 28, 2026
Merged

fix: read EC numbers joined by a semicolon without a space as separate codes #14

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6 changes: 4 additions & 2 deletions src/get_enzyme_data/getECstring.m
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,8 @@
% EC_set : char
% existing EC string to which the EC numbers are appended.
% ecNumbers : char
% space-separated EC numbers associated to the protein.
% EC numbers associated to the protein, separated by white space and/or
% semicolons.
%
% Returns
% -------
Expand All @@ -25,7 +26,8 @@
% --------
% findECInDB
%In case of several ec numbers for the same protein
new_EC_set = replace(strsplit(ecNumbers,' '),';','');
new_EC_set = regexp(strtrim(ecNumbers),'[;\s]+','split');
new_EC_set = new_EC_set(~cellfun(@isempty,new_EC_set));
for l = 1:length(new_EC_set)
EC_set = [EC_set 'EC' new_EC_set{l}];
if l<length(new_EC_set)
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4 changes: 2 additions & 2 deletions test/VerificationMatrix.tsv
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Expand Up @@ -43,10 +43,10 @@ gather_kcats/reviewKcatAssignment.m Has only been tested by running it manually,
gather_kcats/ecStatsFromBrenda.m Not verified against real BRENDA data in this environment -- see its own TODO comment
gather_kcats/mergeKcats.m tc0240
get_enzyme_data/calculateMW.m Not explicitly tested - The code has existed for a long time
get_enzyme_data/findECInDB.m Called from getECfromDatabase - tested when that function is tested; also tc0242, tc0243, tc0244, tc0245
get_enzyme_data/findECInDB.m Called from getECfromDatabase - tested when that function is tested; also tc0242, tc0243, tc0244, tc0245, tc0246
get_enzyme_data/getECfromDatabase.m tc0007 - does not test download of the databases - this is tested in the manual workflows for Yeast-GEM and Human-GEM
get_enzyme_data/getECfromGEM.m tc0006
get_enzyme_data/getECstring.m Called from findECInDB - tested when that function is tested.
get_enzyme_data/getECstring.m Called from findECInDB - tested when that function is tested; also tc0246
download_databases/loadBRENDAdata.m Called from fuzzyKcatMatching - tested when that function is tested; also tc0105, tc0220, tc0221, tc0222
download_databases/fetchBrendaAsset.m tc0085
download_databases/loadDatabases.m Called from getECfromDatabase - tested when that function is tested.
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13 changes: 13 additions & 0 deletions test/unit_tests/parityDecisionTests.m
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Expand Up @@ -89,6 +89,19 @@ function testFindECInDBGeneWithoutECIsLeftOut_tc0245(testCase)
verifyEqual(testCase, EC, '1.1.1.4')
end

function testFindECInDBSplitsCodesOnSemicolons_tc0246(testCase)
% A database cell joins codes with white space, with '; ' or with ';' alone;
% each is read as separate codes.
DBMW = 10000;
geneHashMap = containers.Map({'G1'}, {1});
geneIndex = {1};
cells = {'1.1.1.1 2.2.2.2', '1.1.1.1; 2.2.2.2;', '1.1.1.1;2.2.2.2', ' 1.1.1.1;;2.2.2.2 '};
for i = 1:numel(cells)
EC = findECInDB({'G1'}, cells(i), DBMW, geneIndex, geneHashMap);
verifyEqual(testCase, EC, '1.1.1.1;2.2.2.2')
end
end

function [fuzzy, dlkcat] = originFiveLists()
fuzzy.rxns = {'R1'};
fuzzy.kcats = 5;
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