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fix: yaml eccode annotation handling #613

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Merged
edkerk merged 1 commit into from
Jun 7, 2026
Merged

fix: yaml eccode annotation handling #613

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13 changes: 13 additions & 0 deletions io/readYAMLmodel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -369,6 +369,19 @@
eccodes(ecCodeNo,1:2)={pos,tline_value};
ecCodeNo=ecCodeNo+1;
end
case 'ec-code'
% EC numbers emitted inside the cobra `annotation` block
% (current writer). Captured into model.eccodes the same
% way metabolite `smiles` is pulled out of the annotation
% block; the legacy top-level `eccodes` key above is still
% accepted for older files. A block list of codes follows
% when the value is empty (read via readList='eccodes').
if isempty(tline_value)
readList = 'eccodes';
else
eccodes(ecCodeNo,1:2)={pos,tline_value};
ecCodeNo=ecCodeNo+1;
end
case 'subsystem'
if isempty(tline_value)
readList = 'subsystem';
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78 changes: 53 additions & 25 deletions io/writeYAMLmodel.m
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Expand Up @@ -2,9 +2,11 @@ function writeYAMLmodel(model,fileName,preserveQuotes,sortIds)
% writeYAMLmodel
% Writes a yaml file matching cobrapy's YAML structure. The format is
% cobrapy's native !!omap layout, extended with RAVEN-only top-level
% per-entry keys (inchis, deltaG, metFrom, eccodes, rxnFrom,
% references, confidence_score, protein) and the GECKO ec-rxns /
% ec-enzymes sections. Output is byte-stable with raven_python's
% per-entry keys (inchis, deltaG, metFrom, rxnFrom, references,
% confidence_score, protein) and the GECKO ec-rxns / ec-enzymes
% sections. Reaction EC numbers are written inside the `annotation`
% block as `ec-code` (the cobrapy/geckopy convention), not as a
% top-level reaction key. Output is byte-stable with raven_python's
% io.yaml.write_yaml_model when called with the same model.
%
% model a model structure
Expand Down Expand Up @@ -105,8 +107,9 @@ function writeYAMLmodel(model,fileName,preserveQuotes,sortIds)
%Reactions:
% Field order matches cobrapy + raven_python.io.yaml:
% id, name, metabolites, lower_bound, upper_bound, gene_reaction_rule,
% objective_coefficient, subsystem, notes, annotation,
% then RAVEN-only extras (eccodes, references, rxnFrom, deltaG,
% objective_coefficient, subsystem, notes, annotation (which carries
% the EC numbers under `ec-code`, the cobrapy/geckopy convention),
% then RAVEN-only extras (references, rxnFrom, deltaG,
% confidence_score). The notes key is the canonical `notes` (no
% longer `rxnNotes`); the reader still accepts the legacy key.
fprintf(fid,'- reactions:\n');
Expand All @@ -123,8 +126,7 @@ function writeYAMLmodel(model,fileName,preserveQuotes,sortIds)
end
writeField(model, fid, 'subSystems', 'txt', i, ' - subsystem', preserveQuotes)
writeField(model, fid, 'rxnNotes', 'txt', i, ' - notes', preserveQuotes)
writeField(model, fid, 'rxnMiriams', 'txt', i, ' - annotation', preserveQuotes)
writeField(model, fid, 'eccodes', 'txt', i, ' - eccodes', preserveQuotes)
writeAnnotation(model, fid, 'rxn', i, preserveQuotes)
writeField(model, fid, 'rxnReferences', 'txt', i, ' - references', preserveQuotes)
writeField(model, fid, 'rxnFrom', 'txt', i, ' - rxnFrom', preserveQuotes)
writeField(model, fid, 'rxnDeltaG', 'num', i, ' - deltaG', preserveQuotes)
Expand Down Expand Up @@ -490,40 +492,52 @@ function emitMetaField(fid, key, value, preserveQuotes)

function writeAnnotation(model, fid, kind, pos, preserveQuotes)
% Emit the per-entry `annotation` block, fusing MIRIAM cross-references
% with non-MIRIAM cobrapy-style annotation keys (currently: SMILES for
% metabolites). cobrapy expects SMILES inside `annotation.smiles`, not
% as a top-level metabolite key; this helper keeps the YAML aligned.
% with the non-MIRIAM cobrapy-style annotation keys: `smiles` for
% metabolites and `ec-code` (EC numbers) for reactions. cobrapy and
% geckopy read both from inside `annotation` (not as top-level entry
% keys), so this helper keeps the YAML aligned. `ec-code` is emitted as a
% list — matching cobrapy / raven-python and geckopy, which read it as
% list[str] — even when there is a single code.
switch kind
case 'met'
miriamsField = 'metMiriams';
extraName = 'smiles';
extraField = 'metSmiles';
miriamsField = 'metMiriams';
miriamNamesField = 'newMetMiriamNames';
miriamValsField = 'newMetMiriams';
extraName = 'smiles';
extraField = 'metSmiles';
extraIsList = false;
case 'rxn'
miriamsField = 'rxnMiriams';
miriamNamesField = 'newRxnMiriamNames';
miriamValsField = 'newRxnMiriams';
extraName = 'ec-code';
extraField = 'eccodes';
extraIsList = true;
otherwise
error('writeAnnotation:unsupportedKind', 'Unsupported kind: %s', kind);
end

hasMiriams = isfield(model, miriamsField) && ~isempty(model.(miriamsField){pos});
hasExtra = isfield(model, extraField) && ~isempty(model.(extraField){pos});
hasExtra = isfield(model, extraField) && pos <= numel(model.(extraField)) ...
&& ~isempty(model.(extraField){pos});

if ~hasMiriams && ~hasExtra
return;
end

fprintf(fid, ' - annotation: !!omap\n');
if hasMiriams
% Re-use the writeField MIRIAM path but suppress the block header
% it would emit (we already wrote it above). Tap into the same
% extractMiriam intermediate via a flat fprintf loop.
miriamNames = model.newMetMiriamNames;
miriamValues = model.newMetMiriams;
% Flat fprintf over the extractMiriam intermediate (the block header
% is already written above).
miriamNames = model.(miriamNamesField);
miriamValues = model.(miriamValsField);
for j = 1:size(miriamValues, 2)
v = miriamValues{pos, j};
if isempty(v); continue; end
list = strsplit(strrep(v, ' ', ''), ';');
list = strip(list);
list = strip(strsplit(strrep(v, ' ', ''), ';'));
if numel(list) == 1
valueOut = quoteIfNeeded(list{1}, preserveQuotes);
fprintf(fid, ' - %s: %s\n', miriamNames{j}, valueOut);
fprintf(fid, ' - %s: %s\n', miriamNames{j}, ...
quoteIfNeeded(list{1}, preserveQuotes));
else
fprintf(fid, ' - %s:\n', miriamNames{j});
for k = 1:numel(list)
Expand All @@ -534,8 +548,22 @@ function writeAnnotation(model, fid, kind, pos, preserveQuotes)
end
end
if hasExtra
extraVal = quoteIfNeeded(model.(extraField){pos}, preserveQuotes);
fprintf(fid, ' - %s: %s\n', extraName, extraVal);
if extraIsList
% EC numbers: a ;-joined string -> a block list under `ec-code`
% (always a list, matching cobrapy/raven-python/geckopy).
codes = strip(strsplit(strrep(model.(extraField){pos}, ' ', ''), ';'));
codes = codes(~cellfun('isempty', codes));
if ~isempty(codes)
fprintf(fid, ' - %s:\n', extraName);
for k = 1:numel(codes)
fprintf(fid, ' - %s\n', ...
quoteIfNeeded(codes{k}, preserveQuotes));
end
end
else
fprintf(fid, ' - %s: %s\n', extraName, ...
quoteIfNeeded(model.(extraField){pos}, preserveQuotes));
end
end
end

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