Merge pull request #316 from LCSB-BioCore/mk-cleanup-exchange-stuff

clean up exchanges a bit

src/base/utils/looks_like.jl

@@ -18,17 +18,20 @@ Also see [`find_exchange_reactions`](@ref).
 findall(looks_like_exchange_reaction, reactions(model)) # returns indices
 filter(looks_like_exchange_reaction, reactions(model)) # returns Strings
 
-# to use the optional arguments you need to expand the function's arguments using an anonymous function
+# to use the optional arguments you need to expand the function's arguments
+# using an anonymous function
 findall(x -> looks_like_exchange_reaction(x; exclude_biomass=true), reactions(model)) # returns indices
 filter(x -> looks_like_exchange_reaction(x; exclude_biomass=true), reactions(model)) # returns Strings
 ```
 """
-function looks_like_exchange_reaction(rxn_id::String;
+function looks_like_exchange_reaction(
+    rxn_id::String;
     exclude_biomass = false,
     biomass_strings = _constants.biomass_strings,
     exchange_prefixes = _constants.exchange_prefixes,
 )::Bool
-    any(startswith(rxn_id, x) for x in exchange_prefixes) && !(exclude_biomass && any(occursin(x, rxn_id) for x in biomass_strings))
+    any(startswith(rxn_id, x) for x in exchange_prefixes) &&
+        !(exclude_biomass && any(occursin(x, rxn_id) for x in biomass_strings))
 end
 
 """
@@ -43,7 +46,7 @@ find_exchange_reactions(m::MetabolicModel; kwargs...) =
 """
     find_exchange_reaction_ids(m::MetabolicModel; kwargs...)
 
-Shortcut for finding exchange reaction names in a model; arguments are
+Shortcut for finding exchange reaction identifiers in a model; arguments are
 forwarded to [`looks_like_exchange_reaction`](@ref).
 """
 find_exchange_reaction_ids(m::MetabolicModel; kwargs...) =
@@ -67,12 +70,14 @@ filter(looks_like_biomass_reaction, reactions(model)) # returns strings
 findall(looks_like_biomass_reaction, reactions(model)) # returns indices
 ```
 """
-function looks_like_biomass_reaction(rxn_id::String;
+function looks_like_biomass_reaction(
+    rxn_id::String;
     exclude_exchanges = false,
     exchange_prefixes = _constants.exchange_prefixes,
     biomass_strings = _constants.biomass_strings,
 )::Bool
-    any(occursin(x, rxn_id) for x in biomass_strings) && !(exclude_exchanges && any(startswith(rxn_id, x) for x in exchange_prefixes))
+    any(occursin(x, rxn_id) for x in biomass_strings) &&
+        !(exclude_exchanges && any(startswith(rxn_id, x) for x in exchange_prefixes))
 end
 """
     find_biomass_reactions(m::MetabolicModel; kwargs...)
@@ -86,8 +91,8 @@ find_biomass_reactions(m::MetabolicModel; kwargs...) =
 """
     find_biomass_reaction_ids(m::MetabolicModel; kwargs...)
 
-Shortcut for finding biomass reaction names in a model; arguments are forwarded
-to [`looks_like_biomass_reaction`](@ref).
+Shortcut for finding biomass reaction identifiers in a model; arguments are
+forwarded to [`looks_like_biomass_reaction`](@ref).
 """
 find_biomass_reaction_ids(m::MetabolicModel; kwargs...) =
     filter(id -> looks_like_biomass_reaction(id, kwargs...), reactions(m))
@@ -108,8 +113,26 @@ filter(looks_like_exchange_metabolite, metabolites(model)) # returns strings
 findall(looks_like_exchange_metabolite, metabolites(model)) # returns indices
 ```
 """
-function looks_like_exchange_metabolite(met_id::String;
+function looks_like_exchange_metabolite(
+    met_id::String;
     exchange_suffixes = _constants.exchange_suffixes,
 )::Bool
     any(endswith(met_id, x) for x in exchange_suffixes)
 end
+
+"""
+    find_exchange_metabolites(m::MetabolicModel; kwargs...)
+
+Shortcut for finding exchange metabolite indexes in a model; arguments are
+forwarded to [`looks_like_exchange_metabolite`](@ref).
+"""
+find_exchange_metabolites(m::MetabolicModel; kwargs...) =
+    findall(id -> looks_like_exchange_metabolite(id; kwargs...), metabolites(m))
+"""
+    find_exchange_metabolite_ids(m::MetabolicModel; kwargs...)
+
+Shortcut for finding exchange metabolite identifiers in a model; arguments are
+forwarded to [`looks_like_exchange_metabolite`](@ref).
+"""
+find_exchange_metabolite_ids(m::MetabolicModel; kwargs...) =
+    findall(id -> looks_like_exchange_metabolite(id; kwargs...), metabolites(m))

src/reconstruction/CoreModelCoupled.jl

@@ -381,61 +381,6 @@ function change_coupling_bounds!(
     end
 end
 
-"""
-    find_exchange_reactions(
-        model::CoreModelCoupled;
-        exclude_biomass = false,
-        biomass_str::String = "biomass",
-        exc_prefs = ["EX_"; "Exch_"; "Ex_"],
-    )
-
-Get indices of exchange reactions.
-
-Exchange reactions are identified based on most commonly used prefixes.
-
-"""
-function find_exchange_reactions(
-    model::CoreModelCoupled;
-    exclude_biomass = false,
-    biomass_str::String = "biomass",
-    exc_prefs = ["EX_"; "Exch_"; "Ex_"],
-)
-    return find_exchange_reactions(
-        model.lm;
-        exclude_biomass = exclude_biomass,
-        biomass_str = biomass_str,
-        exc_prefs = exc_prefs,
-    )
-end
-
-"""
-    find_exchange_metabolites(
-        model::CoreModelCoupled;
-        exclude_biomass = false,
-        biomass_str::String = "biomass",
-        exc_prefs = ["EX_"; "Exch_"; "Ex_"],
-    )
-
-Get indices of exchanged metabolites.
-
-In practice returns the metabolites consumed by the reactions given by `find_exchange_reactions`
-and if called with the same arguments, the two outputs correspond.
-
-"""
-function find_exchange_metabolites(
-    model::CoreModelCoupled;
-    exclude_biomass = false,
-    biomass_str::String = "biomass",
-    exc_prefs = ["EX_"; "Exch_"; "Ex_"],
-)
-    return find_exchange_metabolites(
-        model.lm;
-        exclude_biomass = exclude_biomass,
-        biomass_str = biomass_str,
-        exc_prefs = exc_prefs,
-    )
-end
-
 """
     change_bounds!(
         model::CoreModelCoupled,