support yeast-GEM-style indexed compartment names

Closes #691
LCSB-BioCore · Nov 3, 2022 · f42613c · f42613c
1 parent c083ad3
commit f42613c
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Showing 2 changed files with 14 additions and 4 deletions.
diff --git a/src/base/constants.jl b/src/base/constants.jl
@@ -27,6 +27,7 @@ const _constants = (
         metformulas = ["metFormula", "metFormulas"],
         metcharges = ["metCharge", "metCharges"],
         metcompartments = ["metCompartment", "metCompartments", "metComp", "metComps"],
+        metcomptables = ["comps", "compNames"],
         rxnnames = ["rxnNames"],
         metnames = ["metNames"],
     ),

diff --git a/src/base/types/MATModel.jl b/src/base/types/MATModel.jl
@@ -168,10 +168,19 @@ $(TYPEDSIGNATURES)
 
 Extract metabolite compartment from `metCompartment` or `metCompartments`.
 """
-metabolite_compartment(m::MATModel, mid::String) = _maybemap(
-    x -> x[findfirst(==(mid), metabolites(m))],
-    gets(m.mat, nothing, _constants.keynames.metcompartments),
-)
+function metabolite_compartment(m::MATModel, mid::String)
+    res = _maybemap(
+        x -> x[findfirst(==(mid), metabolites(m))],
+        gets(m.mat, nothing, _constants.keynames.metcompartments),
+    )
+    # if the metabolite is an integer or a (very integerish) float, it is an
+    # index to a table of metabolite names (such as in the yeast GEM)
+    typeof(res) <: Real || return res
+    return _maybemap(
+        table -> table[Int(res)],
+        gets(m.mat, nothing, _constants.keynames.metcomptables),
+    )
+end
 
 """
 $(TYPEDSIGNATURES)