feat(mergeupdates): merge new features, functions, and passing tests

.gitignore

@@ -5,4 +5,4 @@
 *.html
 .DS_Store
 .ipynb_checkpoints/
-output
+Manifest.toml

.travis.yml

@@ -1,11 +1,12 @@
+## Documentation: http://docs.travis-ci.com/user/languages/julia/
 language: julia
 
 os:
   - linux
   - osx
 
 julia:
-  - 0.6
+  - 1.1
 
 notifications:
   email: false
@@ -15,19 +16,32 @@ git:
 
 before_script:
   - export PATH=$HOME/.local/bin:$PATH
-
-script:
-  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi		   
-  - julia --check-bounds=yes -e 'Pkg.clone(pwd()); Pkg.pin("Blink", v"0.6.2"); Pkg.pin("PlotlyJS", v"0.10.2"); Pkg.build("Blink"); Pkg.build("ViVa"); Pkg.test("ViVa"; coverage=true)'
-
+
 after_success:
-  - julia -e 'Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
+   - julia -e 'import Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
 
 jobs:
   include:
-    - stage: deploy docs
-      language: julia
+    - stage: "Deploy Documentation"
+      julia: 1.1
+      os: linux
+      script:
+        - julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+        - julia --project=docs/ docs/make.jl
+      after_success: skip
+
+   - stage: Semantic Release
+      if: branch = master AND type != pull_request
+      language: python
       os: linux
-      julia: 0.6
+      python: 3.6
+      before_script: skip
+      install:
+        - pip install typing
+        - pip install python-semantic-release
       script:
-        - julia -e 'Pkg.add("Documenter"); include(joinpath("docs", "make.jl"))'
+        - git config --global user.name "semantic-release (via TravisCI)"
+        - git config --global user.email "semantic-release@travis"
+        - semantic-release publish
+      after_script: skip
+      after_success: skip

Project.toml

@@ -0,0 +1,18 @@
+name = "VIVA"
+uuid = "d7f9f8fa-e687-11e8-2c0b-eb4ab256ef6a"
+authors = ["George Tollefson <[email protected]>"]
+version = "0.0.1"
+
+[deps]
+ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
+Blink = "ad839575-38b3-5650-b840-f874b8c74a25"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+GeneticVariation = "9bc6ac9d-e6b2-5f70-b0a8-242a01662520"
+ORCA = "47be7bcc-f1a6-5447-8b36-7eeeff7534fd"
+PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
+Rsvg = "c4c386cf-5103-5370-be45-f3a111cca3b8"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+julia = ">=0.7"

setup.cfg

@@ -0,0 +1,3 @@
+[semantic_release]
+version_variable=Project.toml:version
+upload_to_pypi=false

src/VIVA.jl

@@ -0,0 +1,92 @@
+module VIVA
+
+using DataFrames
+using PlotlyJS
+using ORCA
+using Rsvg
+using Blink
+using GeneticVariation
+using ArgParse
+using DelimitedFiles
+using Test
+
+#using Base.Filesystem
+
+#include("vcf_utils.jl")
+#include("plot_utils.jl")
+
+#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,
+    clean_column1!,
+    genotype_cell_searcher_maf_correction,
+    genotype_cell_searcher,
+    dp_cell_searcher,
+    load_siglist,
+    sig_list_vcf_filter,
+    chromosome_range_vcf_filter,
+    load_sort_phenotype_matrix,
+    reorder_columns,
+    select_columns,
+    genotype_heatmap2,
+    dp_heatmap2,
+    avg_sample_dp_scatter,
+    avg_variant_dp_line_chart,
+    read_depth_threshhold,
+    list_variant_positions_low_dp,
+    list_sample_names_low_dp,
+    avg_dp_variant,
+    avg_dp_samples,
+    jupyter_main,
+    save_numerical_array,
+    io_pass_filter,
+    io_sig_list_vcf_filter,
+    io_chromosome_range_vcf_filter,
+    generate_genotype_array,
+    define_geno_dict,
+    translate_genotype_to_num_array,
+    translate_readdepth_strings_to_num_array,
+    genotype_heatmap_with_groups,
+    jupyter_main_new,
+    returnXY_column1!,
+    pass_chrrange_siglist_filter,
+    pass_chrrange_filter,
+    pass_siglist_filter,
+    chrrange_siglist_filter,
+    get_sample_names,
+    sortcols_by_phenotype_matrix,
+    find_group_label_indices,
+    checkfor_outputdirectory,
+    combined_all_genotype_array_functions,
+    combined_all_read_depth_array_functions,
+    combined_all_read_depth_array_functions_for_avg_dp,
+    generate_chromosome_positions_for_hover_labels,
+    clean_column1_chr,
+    clean_column1_siglist!,
+    process_plot_inputs,
+    process_plot_inputs_for_grouped_data,
+    returnXY_column1_siglist!,
+    chromosome_label_generator,
+    add_pheno_matrix_to_gt_data_for_plotting,
+    add_pheno_matrix_to_dp_data_for_plotting,
+    generate_hover_text_array,
+    generate_hover_text_array_grouped,
+    save_graphic
+
+#include("vcf_utils.jl")
+include("vcf_utils_complete.jl")
+include("plot_utils.jl")
+include("new_notebook_utils.jl")
+#include("v1_VIVA_notebook_utils.jl")
+#include("io_filters.jl")
+
+end # module

src/ViVa.jl

@@ -1,15 +1,16 @@
-module ViVa
+module VIVA
 
 using DataFrames
 using PlotlyJS
+using ORCA
 using Rsvg
 using Blink
 using GeneticVariation
 using ArgParse
-#using VCFTools
-#using Base.Filesystem
-
+using DelimitedFiles
+using Test
 
+#using Base.Filesystem
 
 #include("vcf_utils.jl")
 #include("plot_utils.jl")
@@ -67,15 +68,25 @@ export
     checkfor_outputdirectory,
     combined_all_genotype_array_functions,
     combined_all_read_depth_array_functions,
+    combined_all_read_depth_array_functions_for_avg_dp,
     generate_chromosome_positions_for_hover_labels,
     clean_column1_chr,
-    clean_column1_siglist!
+    clean_column1_siglist!,
+    process_plot_inputs,
+    process_plot_inputs_for_grouped_data,
+    returnXY_column1_siglist!,
+    chromosome_label_generator,
+    add_pheno_matrix_to_gt_data_for_plotting,
+    add_pheno_matrix_to_dp_data_for_plotting,
+    generate_hover_text_array,
+    generate_hover_text_array_grouped,
+    save_graphic
 
 #include("vcf_utils.jl")
 include("vcf_utils_complete.jl")
 include("plot_utils.jl")
-#include("notebook_utils.jl")
 include("new_notebook_utils.jl")
+#include("v1_VIVA_notebook_utils.jl")
 #include("io_filters.jl")
 
 end # module

src/new_notebook_utils.jl

@@ -1,28 +1,12 @@
 """
-jupyter_main(vcf_filename,field_to_visualize,variant_filter,sample_filter,plot_types,save_format,plot_title,plot_labels)
+jupyter_main(vcf_filename,field_to_visualize,variant_filter,sample_filter,plot_types,save_format,plot_title,plot_labels,output_directory::String)
 
 filters, plots visualization, and saves as figure.
 utilizes all global variables set in first cell of jupyter notebook
 """
 function jupyter_main_new(vcf_filename::String,field_to_visualize::String,variant_filter::Array{String,1},sample_filter::Array{String,1},plot_types::Array{String,1},save_format::String,plot_title::String,output_directory::String)
 
-println("loading packages...")
-
-println("finished loading packages")
-#show stats
-#=
-number_records = nrecords(vcf_filename)
-number_samples = nsamples(vcf_filename)
-
-println("_______________________________________________")
-println()
-println("Summary Statistics of $(parsed_args["vcf_file"])")
-println()
-println("number of records: $number_records")
-println("number of samples: $number_samples")
-println("_______________________________________________")
-println()
-=#
+
 #create vcf reader object
 println("Reading $vcf_filename")
 reader = VCF.Reader(open(vcf_filename, "r")) #reader = VCF.Reader(open("test_4X_191.vcf", "r"))
@@ -255,8 +239,8 @@ elseif field_to_visualize == "read_depth"
        list = ViVa.list_sample_names_low_dp(avg_list, sample_names)
        writedlm(joinpath("$output_directory","Samples_with_low_dp.txt"),list, ",")
        #println("The following samples have read depth of under 15: $list")
-       avg_sample_dp_line_chart(avg_list)
-       graphic = avg_sample_dp_line_chart(avg_list)
+       avg_sample_dp_scatter(avg_list)
+       graphic = avg_sample_dp_scatter(avg_list)
        PlotlyJS.savefig(graphic, joinpath("$output_directory" ,"Average Sample Read Depth.$save_format"))
        return graphic