compartmentalize simulation code and squash overwrite warnings

src/exps/common.jl

@@ -1,3 +1,5 @@
+import CRISPulator: Delta, array_names
+
 function build_parameter_space{T <: ScreenSetup}(::T, parameters::Dict{Symbol, Vector}, num_runs::Int)
     fields = collect(keys(parameters))
     n_fields = length(fields)

src/exps/compare_methods.jl

@@ -1,7 +1,8 @@
 # This experiment will compare the behavior of pvalue, effect size, and
 # product over a wide range of screen and library designs
+import CRISPulator: as_array
 
-function main(filepath; debug=false, quiet=false)
+function compare_methods(filepath; debug=false, quiet=false)
 
     runs = []
 

src/exps/facs_binning.jl

@@ -1,4 +1,4 @@
-function main(filepath; debug=false, quiet=false)
+function facs_binning(filepath; debug=false, quiet=false)
     if !debug
         parameters = Dict{Symbol, Vector}(
             :representation => [10, 100, 1000],

src/exps/facs_binning_snr.jl

@@ -1,4 +1,4 @@
-function main(filepath; debug=false, quiet=false)
+function facs_binning_snr(filepath; debug=false, quiet=false)
     if !debug
         parameters = Dict{Symbol, Vector}(
             :representation => [10, 100, 1000],

src/exps/gen_plots.jl

@@ -6,7 +6,7 @@
 using Gadfly
 using ColorBrewer
 
-function main(filepath; debug=false, quiet=false)
+function gen_plots(filepath; debug=false, quiet=false)
     colors = palette("Accent", 4)
 
     for screentype in [FacsScreen(), GrowthScreen()]

src/exps/growth_bottleneck_snr.jl

@@ -1,4 +1,4 @@
-function main(filepath; debug=false, quiet=false)
+function growth_bottleneck_snr(filepath; debug=false, quiet=false)
     if !debug
         parameters = Dict{Symbol, Vector}(
             :representation => [10, 100, 1000],

src/exps/growth_bottlenecks.jl

@@ -1,4 +1,4 @@
-function main(filepath; debug=false, quiet=false)
+function growth_bottlenecks(filepath; debug=false, quiet=false)
     if !debug
         parameters = Dict{Symbol, Vector}(
             :num_genes => repeat([5000], inner=[3]),

src/exps/growth_representation.jl

@@ -1,4 +1,6 @@
-function main(filepath; debug=false, quiet=false)
+import CRISPulator: flatten_both
+
+function growth_representation(filepath; debug=false, quiet=false)
     if !debug
         parameters = Dict{Symbol, Vector}(
             :representation => [10, 100, 1000],

src/exps/growth_sensitivity_library.jl

@@ -1,8 +1,9 @@
 # Growth screens seem to be highly susceptible to the distribution of
 # genes that promote growth versus that hurt it. This experiment tests
 # the behavior of growth screens under several different library setups
+import CRISPulator: flatten_both
 
-function main(filepath; debug=false, quiet=false)
+function growth_sensitivity_library(filepath; debug=false, quiet=false)
 
     if !debug
 

src/exps/scan_rep_space.jl

@@ -2,7 +2,7 @@
 # is important: at transfection, at the bottleneck(s), and at
 # sequencing.
 
-function main(filepath; debug=false, quiet=false)
+function scan_rep_space(filepath; debug=false, quiet=false)
 
     if !debug
         parameters = Dict{Symbol, Vector}(

src/simulation/load.jl

@@ -1,26 +1,29 @@
-print("Loading simulation framework...")
+"""
+A pooled genetic screen simulator
+"""
+module CRISPulator
 
-packages = [:StatsBase,
-            :Distributions,
-            :DataFrames,
-            :HypothesisTests,
-            :Iterators]
+export ScreenSetup, FacsScreen, GrowthScreen
+export Library, CRISPRi, CRISPRn
+export KDPhenotypeRelationship
+export run_exp
+export auroc, venn, auprc, signal, noise
 
-for package in packages
-    eval(:(using $package))
-    eval(:(@everywhere using $package))
-end
+using StatsBase
+using Distributions
+using DataFrames
+using HypothesisTests
+using Iterators
+using Compat
+import Compat: UTF8String, ASCIIString, view
 
-# Load all simulations files on all workers
-@everywhere function include_all(curr_dir)
-    filenames = ["common.jl", "utils.jl", "library.jl", "transfection.jl",
-                 "selection.jl", "sequencing.jl", "processing.jl",
-                 "designs.jl"]
-    for filename in filenames
-        include(joinpath(curr_dir, filename))
-    end
-end
-curr_dir = Base.source_dir()
-@eval @everywhere include_all($curr_dir)
+include("common.jl")
+include("utils.jl")
+include("library.jl")
+include("transfection.jl")
+include("selection.jl")
+include("sequencing.jl")
+include("processing.jl")
+include("designs.jl")
 
-println("Done.")
+end

src/simulation/utils.jl

@@ -1,4 +1,4 @@
-function Base.count(labels::AbstractArray{Symbol}, pos_labels::Set{Symbol})
+function partition(labels::AbstractArray{Symbol}, pos_labels::Set{Symbol})
     num_pos, num_neg = 0, 0
     for label in labels
         if label in pos_labels
@@ -22,7 +22,7 @@ function auroc(scores::AbstractArray{Float64}, classes::AbstractArray{Symbol},
     num_scores = length(scores)
     ordering = sortperm(scores, rev=rev)
     labels = classes[ordering]
-    num_pos, num_neg = count(labels, pos_labels)
+    num_pos, num_neg = partition(labels, pos_labels)
 
     tprs = Array(Float64, num_scores)
     fprs = Array(Float64, num_scores)
@@ -67,7 +67,7 @@ function auprc(scores::AbstractArray{Float64}, classes::AbstractArray{Symbol},
     num_scores = length(scores) + 1
     ordering = sortperm(scores, rev=rev)
     labels = classes[ordering]
-    num_pos, num_neg = count(labels, pos_labels)
+    num_pos, num_neg = partition(labels, pos_labels)
 
     tn, fn, tp, fp = 0, 0, num_pos, num_neg
 
@@ -114,7 +114,7 @@ function venn(scores::AbstractArray{Float64}, classes::AbstractArray{Symbol},
     num_scores = length(scores)
     ordering = sortperm(scores, rev=rev)
     labels = classes[ordering]
-    num_pos, num_neg = count(labels, pos_labels)
+    num_pos, num_neg = partition(labels, pos_labels)
 
     n_venn = round(Int, num_pos/2)
     n_correct = 0

test/diffcrisprtransfection.jl

@@ -1,3 +1,5 @@
+import CRISPulator: construct_library, build_cells
+
 function convert_cells_to_pop(cells, cell_phenotypes, guides)
     cells_to_phenotypes = [DefaultDict(Float64, Int, 0) for _ in 1:length(guides)]
 

test/growth.jl

@@ -1,4 +1,5 @@
 using StatsBase
+import CRISPulator: grow!
 
 function test_grow_function(phenotypes, expected)
     @assert length(phenotypes) == length(expected)

test/kdrelationships.jl

@@ -1,3 +1,5 @@
+import CRISPulator: Linear, Sigmoidal, response
+
 linear_response = response(Linear())
 
 @test linear_response(0.0, 1.0) == 0.0

test/runtests.jl

@@ -7,10 +7,9 @@ include(normpath(joinpath(Base.source_dir(),"..",load_file)))
 
 using Base.Test
 using DataStructures
-using ColorBrewer
-using Gadfly
-using Compat
-import Compat: UTF8String, ASCIIString, view
+using Distributions
+using DataFrames
+using CRISPulator
 
 println("Running tests:")
 filenames = ["kdrelationships.jl",
@@ -54,7 +53,8 @@ for analysis in analyses
         end
         include(joinpath(analyses_path, analysis))
         tempfile = tempname()
-        main(tempfile, debug=true, quiet=true)
+        func_name = Symbol(splitext(analysis)[1])
+        getfield(Main, func_name)(tempfile, debug=true, quiet=true)
         println("\t\033[1m\033[32mPASSED\033[0m:  $(analysis)")
     catch e
         errorfound = true

test/selectionmethods.jl

@@ -1,3 +1,5 @@
+import CRISPulator: Barcode, select
+
 function testselection(setup)
     N = setup.num_genes
     guides = Barcode[]