Move code common used for benchmarks and tests into Utilities.jl

BioJulia · Jun 10, 2020 · c10623f · c10623f
1 parent 481fe0d
commit c10623f
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Showing 3 changed files with 35 additions and 47 deletions.
diff --git a/benchmark/benchmarks.jl b/benchmark/benchmarks.jl
@@ -11,31 +11,6 @@ N = 1000
 SEED = 1234
 SEQNAMES = "chr" .* string.(1:3)
 
-# Generate an array of n random Interval{Int} object. With sequence names
-# samples from seqnames, and intervals drawn to lie in [1, maxpos].
-function random_intervals(seqnames::Vector{String}, maxpos::Int, n::Int)
-    seq_dist = Categorical(length(seqnames))
-    strand_dist = Categorical(2)
-    length_dist = Normal(1000, 1000)
-    intervals = Vector{Interval{Int}}(undef, n)
-    for i in 1:n
-        intlen = maxpos
-        while intlen >= maxpos || intlen <= 0
-            intlen = ceil(Int, rand(length_dist))
-        end
-        first = rand(1:maxpos-intlen)
-        last = first + intlen - 1
-        strand = rand(strand_dist) == 1 ? STRAND_POS : STRAND_NEG
-        intervals[i] = Interval{Int}(seqnames[rand(seq_dist)], first, last, strand, i)
-    end
-    return intervals
-end
-
-function random_intervals(seqnames::Vector{String}, maxpos::Int, n::Int, seed::Int)
-    Random.seed!(seed)
-    return random_intervals(seqnames, maxpos, n)
-end
-
 intervals = random_intervals(SEQNAMES, 1000, N, SEED)
 intervals_sorted = sort(intervals)
 

diff --git a/test/Utilities.jl b/test/Utilities.jl
@@ -0,0 +1,32 @@
+module Utilities
+
+using Distributions
+using GenomicFeatures
+using Random
+
+# Generate an array of n random Interval{Int} object. With sequence names
+# samples from seqnames, and intervals drawn to lie in [1, maxpos].
+function random_intervals(seqnames::Vector{String}, maxpos::Int, n::Int)
+    seq_dist = Categorical(length(seqnames))
+    strand_dist = Categorical(2)
+    length_dist = Normal(1000, 1000)
+    intervals = Vector{Interval{Int}}(undef, n)
+    for i in 1:n
+        intlen = maxpos
+        while intlen >= maxpos || intlen <= 0
+            intlen = ceil(Int, rand(length_dist))
+        end
+        first = rand(1:maxpos-intlen)
+        last = first + intlen - 1
+        strand = rand(strand_dist) == 1 ? STRAND_POS : STRAND_NEG
+        intervals[i] = Interval{Int}(seqnames[rand(seq_dist)], first, last, strand, i)
+    end
+    return intervals
+end
+
+function random_intervals(seqnames::Vector{String}, maxpos::Int, n::Int, seed::Int)
+    Random.seed!(seed)
+    return random_intervals(seqnames, maxpos, n)
+end
+
+end  # module Utilities
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,9 +1,11 @@
 using GenomicFeatures
 using Test
 
-using Distributions
 import Random
 
+include(joinpath(@__DIR__, "Utilities.jl"))
+import .Utilities: random_intervals
+
 
 # Test that an array of intervals is well ordered
 function is_all_ordered(intervals::Vector{I}) where I <: Interval
@@ -15,27 +17,6 @@ function is_all_ordered(intervals::Vector{I}) where I <: Interval
     return true
 end
 
-# Generate an array of n random Interval{Int} object. With sequence names
-# samples from seqnames, and intervals drawn to lie in [1, maxpos].
-function random_intervals(seqnames, maxpos::Int, n::Int)
-    seq_dist = Categorical(length(seqnames))
-    strand_dist = Categorical(2)
-    length_dist = Normal(1000, 1000)
-    intervals = Vector{Interval{Int}}(undef, n)
-    for i in 1:n
-        intlen = maxpos
-        while intlen >= maxpos || intlen <= 0
-            intlen = ceil(Int, rand(length_dist))
-        end
-        first = rand(1:maxpos-intlen)
-        last = first + intlen - 1
-        strand = rand(strand_dist) == 1 ? STRAND_POS : STRAND_NEG
-        intervals[i] = Interval{Int}(seqnames[rand(seq_dist)],
-                                     first, last, strand, i)
-    end
-    return intervals
-end
-
 # A simple interval intersection implementation to test against.
 function simple_intersection(intervals_a, intervals_b; filter=(a,b)->true)
     sort!(intervals_a)