Merge pull request #15 from himoto/develop

Hiroaki Imoto · web-flow · commit f74bf693bf6e · 2020-11-19T09:56:04.000+09:00
Fix index in set_search_param.jl
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "BioMASS"
 uuid = "324734c7-f323-4536-9335-775d9be9d101"
 authors = ["Hiroaki Imoto <himoto@protein.osaka-u.ac.jp>"]
-version = "0.2.0"
+version = "0.2.1"
 
 [deps]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
diff --git a/fos_model/fitness.jl b/fos_model/fitness.jl
@@ -77,104 +77,13 @@ function objective(indiv_gene::Vector{Float64})::Float64
                         Exp.experiments[i],
                         Exp.get_timepoint(obs_name),
                         Sim.conditions,
-                        sim_norm_max = (
-                            length(Sim.normalization) == 0 ? 1.0 : norm_max
+                        sim_norm_max = ifelse(
+                            length(Sim.normalization) == 0, 1.0, norm_max
                         )
                     )...
                 )
             end
         end
-        #=
-        error::Vector{Float64} = zeros(16)
-
-        sim_norm_max = maximum(Sim.simulations[observables_index("Phosphorylated_MEKc"),:,:])
-        exp_t = Exp.get_timepoint(observables_index("Phosphorylated_MEKc"))
-        error[1] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_MEKc"), Int.(exp_t.+1), conditions_index("EGF")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_MEKc")]["EGF"]
-        )
-        error[2] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_MEKc"), Int.(exp_t.+1), conditions_index("HRG")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_MEKc")]["HRG"]
-        )
-
-        sim_norm_max = maximum(Sim.simulations[observables_index("Phosphorylated_ERKc"),:,:])
-        exp_t = Exp.get_timepoint(observables_index("Phosphorylated_ERKc"))
-        error[3] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_ERKc"), Int.(exp_t.+1), conditions_index("EGF")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_ERKc")]["EGF"]
-        )
-        error[4] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_ERKc"), Int.(exp_t.+1), conditions_index("HRG")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_ERKc")]["HRG"]
-        )
-
-        sim_norm_max = maximum(Sim.simulations[observables_index("Phosphorylated_RSKw"),:,:])
-        exp_t = Exp.get_timepoint(observables_index("Phosphorylated_RSKw"))
-        error[5] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_RSKw"), Int.(exp_t.+1), conditions_index("EGF")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_RSKw")]["EGF"]
-        )
-        error[6] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_RSKw"), Int.(exp_t.+1), conditions_index("HRG")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_RSKw")]["HRG"]
-        )
-
-        sim_norm_max = maximum(Sim.simulations[observables_index("Phosphorylated_CREBw"),:,:])
-        exp_t = Exp.get_timepoint(observables_index("Phosphorylated_CREBw"))
-        error[7] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_CREBw"), Int.(exp_t.+1), conditions_index("EGF")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_CREBw")]["EGF"]
-        )
-        error[8] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_CREBw"), Int.(exp_t.+1), conditions_index("HRG")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_CREBw")]["HRG"]
-        )
-
-        sim_norm_max = maximum(Sim.simulations[observables_index("dusp_mRNA"),:,:])
-        exp_t = Exp.get_timepoint(observables_index("dusp_mRNA"))
-        error[9] = compute_objval_rss(
-            Sim.simulations[observables_index("dusp_mRNA"), Int.(exp_t.+1), conditions_index("EGF")]./sim_norm_max,
-            Exp.experiments[observables_index("dusp_mRNA")]["EGF"]
-        )
-        error[10] = compute_objval_rss(
-            Sim.simulations[observables_index("dusp_mRNA"), Int.(exp_t.+1), conditions_index("HRG")]./sim_norm_max,
-            Exp.experiments[observables_index("dusp_mRNA")]["HRG"]
-        )
-
-        sim_norm_max = maximum(Sim.simulations[observables_index("cfos_mRNA"),:,:])
-        exp_t = Exp.get_timepoint(observables_index("cfos_mRNA"))
-        error[11] = compute_objval_rss(
-            Sim.simulations[observables_index("cfos_mRNA"), Int.(exp_t.+1), conditions_index("EGF")]./sim_norm_max,
-            Exp.experiments[observables_index("cfos_mRNA")]["EGF"]
-        )
-        error[12] = compute_objval_rss(
-            Sim.simulations[observables_index("cfos_mRNA"), Int.(exp_t.+1), conditions_index("HRG")]./sim_norm_max,
-            Exp.experiments[observables_index("cfos_mRNA")]["HRG"]
-        )
-
-        sim_norm_max = maximum(Sim.simulations[observables_index("cFos_Protein"),:,:])
-        exp_t = Exp.get_timepoint(observables_index("cFos_Protein"))
-        error[13] = compute_objval_rss(
-            Sim.simulations[observables_index("cFos_Protein"), Int.(exp_t.+1), conditions_index("EGF")]./sim_norm_max,
-            Exp.experiments[observables_index("cFos_Protein")]["EGF"]
-        )
-        error[14] = compute_objval_rss(
-            Sim.simulations[observables_index("cFos_Protein"), Int.(exp_t.+1), conditions_index("HRG")]./sim_norm_max,
-            Exp.experiments[observables_index("cFos_Protein")]["HRG"]
-        )
-
-        sim_norm_max = maximum(Sim.simulations[observables_index("Phosphorylated_cFos"),:,:])
-        exp_t = Exp.get_timepoint(observables_index("Phosphorylated_cFos"))
-        error[15] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_cFos"), Int.(exp_t.+1), conditions_index("EGF")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_cFos")]["EGF"]
-        )
-        error[16] = compute_objval_rss(
-            Sim.simulations[observables_index("Phosphorylated_cFos"), Int.(exp_t.+1), conditions_index("HRG")]./sim_norm_max,
-            Exp.experiments[observables_index("Phosphorylated_cFos")]["HRG"]
-        )
-        =#
         return sum(error)
     else
         return Inf
diff --git a/fos_model/set_search_param.jl b/fos_model/set_search_param.jl
@@ -378,7 +378,7 @@ function conv_lin2log!(
     )
     if length(difference) > 0
         for idx in difference
-            if j <= C.NUM
+            if idx <= C.NUM
                 println(@sprintf("`C.%s`", C.NAMES[Int(idx)]))
             else
                 println(@sprintf("`V.%s`", V.NAMES[Int(idx)-C.NUM]))

Original file line number	Diff line number	Diff line change
`@@ -378,7 +378,7 @@ function conv_lin2log!(`
`378`	`378`	`)`
`379`	`379`	`if length(difference) > 0`
`380`	`380`	`for idx in difference`
`381`		`- if j <= C.NUM`
	`381`	`+ if idx <= C.NUM`
`382`	`382`	println(@sprintf("`C.%s`", C.NAMES[Int(idx)]))
`383`	`383`	`else`
`384`	`384`	println(@sprintf("`V.%s`", V.NAMES[Int(idx)-C.NUM]))