feat(FixTestsToAccomodateNewFunctionNames.): renamed functions in viv…

…a executable, src files, and tests makes terminology consistent with paper
compbiocore · Mar 19, 2019 · 959b2b0 · 959b2b0
1 parent e3231d3
commit 959b2b0
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Showing 16 changed files with 41 additions and 890 deletions.
diff --git a/src/VIVA.jl b/src/VIVA.jl
@@ -17,13 +17,6 @@ using Test
 
 #end #module
 
-#=
-const g_white = "400" #homo reference 0/0
-const g_red = "800" #homo variant 1/1 1/2 2/2 1/3 2/3 3/3 4/4 5/5 6/6 etc
-const g_pink = "600" #hetero variant 0/1 1/0 0/2 2/0 etc
-const g_blue = "0" #no call ./.
-=#
-
 export
     format_reader,
     load_vcf,
@@ -80,8 +73,7 @@ export
     add_pheno_matrix_to_dp_data_for_plotting,
     generate_hover_text_array,
     generate_hover_text_array_grouped,
-    save_graphic,
-    alias
+    save_graphic
 
 #include("vcf_utils.jl")
 include("vcf_utils_complete.jl")

diff --git a/src/vcf_utils_complete.jl b/src/vcf_utils_complete.jl
@@ -17,7 +17,7 @@ end
 
 """
     clean_column1_siglist!(siglist)
-    replaces "X","Y","M" with 23,24,25 {Int}
+Replaces strings "X","Y","M" with 23,24,25 {Int} in array generated in load_siglist()
 use in load_siglist() because X and Y need to be replaced with Int
 """
 function clean_column1_siglist!(siglist)
@@ -1476,13 +1476,15 @@ return(hover_text_array)
 end
 
 """
-    save_graphic(graphic,output_directory,save_ext,title)
+    save_graphic(graphic,output_directory,save_ext,title,remote_option)
 Save plot in either html or static image formats incuding eps, png, svg, and pdf
 """
-function save_graphic(graphic,output_directory,save_ext,title)
+function save_graphic(graphic,output_directory,save_ext,title,remote_option)
 
-    if save_ext=="html"
+    if save_ext=="html" && remote_option == true
         PlotlyJS.savehtml(graphic, joinpath("$(output_directory)" ,"$title.$(save_ext)"), :remote)
+    elseif save_ext=="html" && remote_option != true
+        PlotlyJS.savehtml(graphic, joinpath("$(output_directory)" ,"$title.$(save_ext)"))
     elseif save_ext != "html"
         PlotlyJS.savefig(graphic, joinpath("$(output_directory)" ,"$title.$(save_ext)"))
     end

diff --git a/test/.DS_Store b/test/.DS_Store
diff --git a/test/new_vcf_utils.jl b/test/new_vcf_utils.jl
@@ -12,10 +12,10 @@ julia> Pkg.test(pkg_for"VIVA")
 @testset "VCFUtils" begin
 
 vcf_filename = "test_files/test_4X_191.vcf"
-vcf_filename_with_chr = "test_files/test_with_chr.vcf"
+#vcf_filename_with_chr = "test_files/test_with_chr.vcf"
 
 reader = VCF.Reader(open(vcf_filename, "r"))
-reader_with_chr = VCF.Reader(open(vcf_filename_with_chr, "r"))
+#reader_with_chr = VCF.Reader(open(vcf_filename_with_chr, "r"))
 sample_names = get_sample_names(reader)
 
 dp_limit = 50
@@ -30,23 +30,23 @@ end
 
 #functions for variant filters
 
-@testset "io_chromosome_range_vcf_filter" begin
-sub = io_chromosome_range_vcf_filter("chr4:0-400000000",vcf_filename)
+@testset "io_genomic_range_vcf_filter" begin
+sub = io_genomic_range_vcf_filter("chr4:0-400000000",vcf_filename)
 @test typeof(sub) == Array{Any,1}
 @test size(sub,1) == 1012
-#println("io_chromosome_range_vcf_filter type is $(typeof(sub))")
-#println("io_chromosome_range_vcf_filter size is $(size(sub,1))")
+#println("io_genomic_range_vcf_filter type is $(typeof(sub))")
+#println("io_genomic_range_vcf_filter size is $(size(sub,1))")
 end
 
 
 @testset "filters_with_siglist" begin
 
     @testset "load_siglist" begin
-    sig_list=load_siglist("test_files/sig_list_for_test.csv")
+    sig_list=load_siglist("test_files/positions_list.csv")
 
-    @testset "pass_chrrange_siglist_filter" begin
-    sig_list=load_siglist("test_files/sig_list_for_test.csv")
-    sub = pass_chrrange_siglist_filter(vcf_filename,sig_list,"chr4:0-5000000000")
+    @testset "pass_genomic_range_siglist_filter" begin
+    sig_list=load_siglist("test_files/positions_list.csv")
+    sub = pass_genomic_range_siglist_filter(vcf_filename,sig_list,"chr4:0-5000000000")
 
     @test (typeof(sub[1])) == GeneticVariation.VCF.Record
     @test (length(sub)) ==  5
@@ -66,8 +66,8 @@ end
             @test (length(sub)) ==  10
             end
 
-            @testset "chrrange_siglist_filter" begin
-            sub = chrrange_siglist_filter(vcf_filename,sig_list,"chr4:0-400000000")
+            @testset "genomic_range_siglist_filter" begin
+            sub = genomic_range_siglist_filter(vcf_filename,sig_list,"chr4:0-400000000")
             @test (typeof(sub[1])) == GeneticVariation.VCF.Record
             @test (length(sub)) ==  5
             end
@@ -82,9 +82,9 @@ end
     @test (length(sub)) ==  1164
 end
 
-@testset "pass_chrrange_filter" begin
+@testset "pass_genomic_range_filter" begin
     reader = VCF.Reader(open(vcf_filename, "r"))
-    sub = pass_chrrange_filter(reader,"chr4:0-400000000",vcf_filename)
+    sub = pass_genomic_range_filter(reader,"chr4:0-400000000",vcf_filename)
     @test (typeof(sub[1])) == GeneticVariation.VCF.Record
     @test (length(sub)) ==  856
 end
@@ -220,7 +220,7 @@ dp_num_array,dp_chromosome_labels=combined_all_read_depth_array_functions(sub)
     end
 
     @testset "sortcols_by_phenotype_matrix" begin
-    vcf,group_label_pack=sortcols_by_phenotype_matrix("test_files/fixed_pheno_matrix_test.csv","case,control", dp_num_array, sample_names)
+    vcf,group_label_pack=sortcols_by_phenotype_matrix("test_files/sample_metadata_matrix.csv","case,control", dp_num_array, sample_names)
     #println("sortcols_by_phenotype_matrix vcf type is $(typeof(vcf))")
     #println("sortcols_by_phenotype_matrix vcf size is $(size(vcf,1))")
     #println("sortcols_by_phenotype_matrix group_label_pack type is $(typeof(group_label_pack))")

diff --git a/test/test_files/test_with_chr.vcf → test/test_files/chr_format.vcf b/test/test_files/test_with_chr.vcf → test/test_files/chr_format.vcf
diff --git a/test/test_files/pheno_matrix_chr.csv b/test/test_files/pheno_matrix_chr.csv
diff --git a/test/test_files/sig_list_for_test.csv → test/test_files/positions_list.csv b/test/test_files/sig_list_for_test.csv → test/test_files/positions_list.csv
diff --git a/test/test_files/positions_list_test_4X_191.csv b/test/test_files/positions_list_test_4X_191.csv
diff --git a/test/test_files/fixed_pheno_matrix_test.csv → test/test_files/sample_metadata_matrix.csv b/test/test_files/fixed_pheno_matrix_test.csv → test/test_files/sample_metadata_matrix.csv
diff --git a/test/test_files/sample_order_list_fortest.txt b/test/test_files/sample_order_list_fortest.txt
diff --git a/test/test_files/sample_phenotype_matrix.csv b/test/test_files/sample_phenotype_matrix.csv
diff --git a/test/test_files/select_samples_list.txt b/test/test_files/select_samples_list.txt
@@ -1 +1 @@
-cas1001	cas1003	cas1005	cas1010	cas1012
+cas1001	cas1003	cas1005	cas1010	cas1012
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		cas1001 cas1003 cas1005 cas1010 cas1012
		cas1001 cas1003 cas1005 cas1010 cas1012