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refactor: adjust extractAllianceGenomeOrthologs from reading JSON to TSV file #482

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merged 7 commits into from
Feb 21, 2023
Merged

refactor: adjust extractAllianceGenomeOrthologs from reading JSON to TSV file #482

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72cc59f
feat: deprecate code for loading Json input file
haowang-bioinfo Feb 15, 2023
e2a5f78
refactor: read fieldList directly from the cell structure
haowang-bioinfo Feb 15, 2023
2af83ca
fix: replace cell2mat with str2double for robustness
haowang-bioinfo Feb 15, 2023
e96414b
Merge branch 'develop' into feat/changeOG2TSV
haowang-bioinfo Feb 16, 2023
78c4f7d
doc: replace JSON with TSV in documentation
haowang-bioinfo Feb 18, 2023
b35c3af
update README.md [skip ci]
haowang-bioinfo Feb 20, 2023
2539b2e
update .all-contributorsrc [skip ci]
haowang-bioinfo Feb 20, 2023
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35 changes: 4 additions & 31 deletions code/GPRs/extractAllianceGenomeOrthologs.m
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Original file line number Diff line number Diff line change
Expand Up @@ -42,37 +42,10 @@
error('Input file %s cannot be found',string(homologFilename));
end

% load input file
inputPairs = jsondecode(fileread(homologFilename));

% define output structure
fieldList = {'fromGeneId',
'fromSymbol'
'toGeneId',
'toSymbol',
'best',
'bestReverse',
'methodCount',
'totalMethodCount'};


% initialize output structure
for i = 1:length(fieldList)
orthologStructure.(fieldList{i}) = {};
end


% loop through the content to extract corresponding values
for i=1:length(inputPairs.results)
orthologStructure.fromGeneId = [orthologStructure.fromGeneId; inputPairs.results(i).gene.id];
orthologStructure.fromSymbol = [orthologStructure.fromSymbol; inputPairs.results(i).gene.symbol];
orthologStructure.toGeneId = [orthologStructure.toGeneId; inputPairs.results(i).homologGene.id];
orthologStructure.toSymbol = [orthologStructure.toSymbol; inputPairs.results(i).homologGene.symbol];
for j = 5:length(fieldList)
orthologStructure.(fieldList{j}) = [orthologStructure.(fieldList{j}); inputPairs.results(i).(fieldList{j})];
end
end

% load orthologStructure directly from tsv file
orthologStructure = importTsvFile(homologFilename);
fieldList = fieldnames(orthologStructure);

% check countBest
if countBest
Expand Down Expand Up @@ -119,7 +92,7 @@
% if the pairs are neither bestForward nor bestReverse, then only
% reserve the one with highest number of methodCount
if noBestForwardReverse
[~, topMethodCount]=maxk(cell2mat(orthologStructure.methodCount(indMore)), 1);
[~, topMethodCount]=maxk(str2double(orthologStructure.methodCount(indMore)), 1);
output.from = [output.from; orthologStructure.fromSymbol{indMore(topMethodCount)}];
output.to = [output.to; orthologStructure.toSymbol{indMore(topMethodCount)}];
end
Expand Down