From a4b6f334294797ca87db4b70af2cd7f406ff92f3 Mon Sep 17 00:00:00 2001
From: George Tollefson <gatollefson@gmail.com>
Date: Thu, 1 Nov 2018 16:12:35 -0400
Subject: [PATCH 1/6] finished most tests. Fixed siglist filter.
---
src/ViVa.jl | 2 +-
src/vcf_utils_complete.jl | 13 +-
test/.DS_Store | Bin 8196 -> 8196 bytes
test/new_vcf_utils.jl | 244 ++++++++----------
...olumn_list.txt => select_samples_list.txt} | 0
viva_cli.jl | 13 +-
6 files changed, 124 insertions(+), 148 deletions(-)
rename test/test_files/{select_column_list.txt => select_samples_list.txt} (100%)
diff --git a/src/ViVa.jl b/src/ViVa.jl
index 67780f7..be303b2 100644
--- a/src/ViVa.jl
+++ b/src/ViVa.jl
@@ -4,7 +4,7 @@ using DataFrames #use CSV.jl ? depwarnings
using PlotlyJS
using Rsvg
using Blink
-using CSV
+#using CSV
using GeneticVariation
using ArgParse
using VCFTools
diff --git a/src/vcf_utils_complete.jl b/src/vcf_utils_complete.jl
index 68b749b..fb8964e 100644
--- a/src/vcf_utils_complete.jl
+++ b/src/vcf_utils_complete.jl
@@ -51,7 +51,6 @@ function sort_genotype_array(genotype_array)
data=genotype_array[:,3:size(genotype_array,2)]
chrom_positions = [parse(Int, i) for i in genotype_array[:,1:2]]
genotype_array = hcat(chrom_positions,data)
-
genotype_array = sortrows(genotype_array, by=x->(x[1],x[2]))
return genotype_array
@@ -122,16 +121,18 @@ function io_sig_list_vcf_filter(sig_list,vcf_filename)
pos=(sig_list[row,2])
reader = VCF.Reader(open(vcf_filename, "r"))
-
+ tic()
for record in reader
if typeof(VCF.chrom(record)) == String
chr = string(chr)
-
if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos)
push!(vcf_subarray,record)
end
+
+ end#remove this if need code below
+#=
else
if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos)
@@ -139,7 +140,9 @@ function io_sig_list_vcf_filter(sig_list,vcf_filename)
end
end
+ =#
end
+ toc()
end
return vcf_subarray
@@ -367,9 +370,7 @@ convert sub from variant filters to gt_num_array and gt_chromosome_labels for pl
"""
function combined_all_genotype_array_functions(sub)
genotype_array = generate_genotype_array(sub,"GT")
-
map!(s->replace(s, "chr", ""), genotype_array, genotype_array)
-
clean_column1!(genotype_array)
genotype_array=ViVa.sort_genotype_array(genotype_array)
geno_dict = define_geno_dict()
@@ -508,7 +509,7 @@ function get_sample_names(reader)
end
"""
- find_group_label_indices(pheno)
+ find_group_label_indices(pheno,trait_to_group_by,row_to_sort_by)
find indices and determines names for group 1 and group 2 labels on plots. finds index of center of each sample group to place tick mark and label.
"""
function find_group_label_indices(pheno,trait_to_group_by,row_to_sort_by)
diff --git a/test/.DS_Store b/test/.DS_Store
index e9bcd34daba8bc5a670b0d044f29f56de51d96ab..c02d3ce4ddfb142ddb2f95a94384b282c69c667d 100644
GIT binary patch
delta 16
XcmZp1XmQxES8(!r0m;qR1oij;I<5vt
delta 18
ZcmZp1XmQxESCEl$@&*Bk&DR9=_y9oD21)<`
diff --git a/test/new_vcf_utils.jl b/test/new_vcf_utils.jl
index a0ee61b..a0825e9 100644
--- a/test/new_vcf_utils.jl
+++ b/test/new_vcf_utils.jl
@@ -26,18 +26,21 @@ sample_names = get_sample_names(reader)
@test df[3,1] == 2
end
+#functions for variant filters
+
@testset "io_chromosome_range_vcf_filter" begin
sub = io_chromosome_range_vcf_filter("chr4:0-400000000",reader)
println(sub[1:2])
println(size(sub,2))
end
-@testset "io_sig_list_vcf_filter" begin
+#=
+@testset "filters_with_siglist" begin
@testset "load_siglist" begin
- sig_list=load_siglist("test_files/significantList_for_proteinstructures.csv")
- println(sig_list[2:1])
- println(size(sig_list,1))
+ sig_list=load_siglist("test_files/significantList_for_proteinstructures.csv")
+ println(sig_list[2:1])
+ println(size(sig_list,1))
@testset "clean_column1_siglist!" begin
clean_column1_siglist!(sig_list)
@@ -45,170 +48,145 @@ end
println(size(sig_list,1))
end
- sub=io_sig_list_vcf_filter(sig_list,vcf_filename)
- println(sub[1,5])
-
- @testset "pass_chrrange_siglist_filter" begin
- sub = pass_chrrange_siglist_filter(vcf_filename,sig_list,"chr4:0-400000000")
- println(sub[1,5])
+ @testset "io_sig_list_vcf_filter" begin
+ sub=io_sig_list_vcf_filter(sig_list,vcf_filename)
+ @test (typeof(sub[1])) == GeneticVariation.VCF.Record
+ @test (length(sub)) == 13
+ end
- @testset pass_siglist_filter begin
- sub = pass_siglist_filter(vcf_filename,sig_list)
- end
+ @testset "pass_chrrange_siglist_filter" begin
+ sub = pass_chrrange_siglist_filter(vcf_filename,sig_list,"chr4:0-400000000")
+ @test (typeof(sub[1])) == GeneticVariation.VCF.Record
+ @test (length(sub)) == 12
+ end
- @testset "chrrange_siglist_filter" begin
- sub = chrrange_siglist_filter(vcf_filename,sig_list,"chr4:0-400000000")
- end
+ @testset "pass_siglist_filter" begin
+ sub = pass_siglist_filter(vcf_filename, sig_list)
+ @test (typeof(sub[1])) == GeneticVariation.VCF.Record
+ @test (length(sub)) == 12
+ end
+ @testset "chrrange_siglist_filter" begin
+ sub = chrrange_siglist_filter(vcf_filename,sig_list,"chr4:0-400000000")
+ @test (typeof(sub[1])) == GeneticVariation.VCF.Record
+ @test (length(sub)) == 13
+ end
- end
+ end
end
-end
+=#
@testset "io_pass_filter" begin
+ reader = VCF.Reader(open(vcf_filename, "r"))
sub = io_pass_filter(reader)
- println(sub[2,1])
+ @test (typeof(sub[1])) == GeneticVariation.VCF.Record
+ @test (length(sub)) == 1164
end
@testset "pass_chrrange_filter" begin
+ reader = VCF.Reader(open(vcf_filename, "r"))
sub = pass_chrrange_filter(reader,"chr4:0-400000000")
+ @test (typeof(sub[1])) == GeneticVariation.VCF.Record
+ @test (length(sub)) == 856
end
-
-
-
-
-
-#=
-#functions for variant filters
-
-
#functions for converting vcf record array to numerical array
+@testset "combined_all_genotype_array_functions" begin
-"""
- create_chr_dict()
-creates dict for use in combined_all_genotype_array_functions() for removing 'chr' from chromosome labels to allow sorting variant records by chromosome position.
-"""
-@testset create_chr_dict() begin
-
-end
-
-"""
- combined_all_genotype_array_functions(sub)
-convert sub from variant filters to gt_num_array and gt_chromosome_labels for plot functions.
-"""
-@testset combined_all_genotype_array_functions(sub) begin
-
-end
-
-"""
- combined_all_read_depth_array_functions(sub)
-convert sub from variant filters to dp_num_array and dp_chromosome_labels for plot functions.
-"""
-@testset combined_all_read_depth_array_functions(sub) begin
-
-end
-
-"""
- generate_genotype_array(record_sub::Array{Any,1},genotype_field::String)
-Returns numerical array of genotype values (either genotype or read_depth values) which are translated by another function into num_array
-Where genotype_field is either GT or DP to visualize genotype or read_depth
-"""
-@testset generate_genotype_array(record_sub::Array{Any,1},y) begin
-
-end
-
-"""
- define_geno_dict()
-returns dictionary of values for use in replace_genotype_with_vals()
-"""
-@testset define_geno_dict() begin
+reader = VCF.Reader(open(vcf_filename, "r"))
+sub = io_pass_filter(reader)
-end
+gt_num_array,gt_chromosome_labels=combined_all_genotype_array_functions(sub)
+println(typeof(gt_num_array))
+println(length(gt_num_array))
+println(typeof(gt_chromosome_labels))
+println(length(gt_chromosome_labels))
-"""
- translate_genotype_to_num_array(genotype_array,geno_dict)
-returns a tuple of num_array for plotting, and chromosome labels for plotting as label bar.
-Translates array of genotype values to numerical array of categorical values.
-Genotype values are converted to categorical values. No_call=0, 0/0=400, heterozygous_variant=600, homozygous_variant=800
-"""
-@testset translate_genotype_to_num_array(genotype_array,geno_dict) begin
+ @testset "generate_genotype_array" begin
+ reader = VCF.Reader(open(vcf_filename, "r"))
+ sub = io_pass_filter(reader)
+ genotype_array=generate_genotype_array(sub,"GT")
+ println(typeof(genotype_array))
+ println(length(genotype_array))
+ println(genotype_array[3:5])
+
+ @testset "define_geno_dict" begin
+ geno_dict = define_geno_dict()
+ println(typeof(geno_dict))
+ println(length(geno_dict))
+
+ @testset "translate_genotype_to_num_array" begin
+ gt_num_array,gt_chromosome_labels=translate_genotype_to_num_array(genotype_array,geno_dict)
+ println(typeof(gt_num_array))
+ println(length(gt_num_array))
+ println(typeof(gt_chromosome_labels))
+ println(length(gt_chromosome_labels))
+ end
+ end
+ end
end
-"""
- translate_readdepth_strings_to_num_array(read_depth_array::Array{Any,2})
-Returns array of read_depth as int for plotting and average calculation.
-By default, read depth values over 100 are replaced with 100 to improve heatmap visualization (see read_depth_threshhold() ).
-Where read_depth_array is output of generate_genotype_array() for DP option
-returns a tuple of num_array type Int for average calculation and plotting, and chromosome labels for plotting as label bar
-"""
-@testset translate_readdepth_strings_to_num_array(read_depth_array::Array{Any,2}) begin
+@testset "combined_all_read_depth_array_functions" begin #inside functions same used in combined_all_genotype_array_functions
+reader = VCF.Reader(open(vcf_filename, "r"))
+sub = io_pass_filter(reader)
+dp_num_array,dp_chromosome_labels=combined_all_read_depth_array_functions(sub)
+println(typeof(dp_num_array))
+println(length(dp_num_array))
+println(typeof(dp_chromosome_labels))
+println(length(dp_chromosome_labels))
+
+@testset "get_sample_names" begin
+reader = VCF.Reader(open(vcf_filename, "r"))
+sample_names=get_sample_names(reader)
+println("get_sample_names")
+println(typeof(sample_names))
+println(length(sample_names))
+
+@testset "avg_dp_samples" begin
+avg_sample_list=avg_dp_samples(dp_num_array)
+println("avg_sample_list is $avg_sample_list")
+
+@testset "list_sample_names_low_dp" begin
+list=list_sample_names_low_dp(avg_sample_list,sample_names)
+println(list)
end
-
-#functions for sample filters
-
-"""
- get_sample_names(reader)
-returns sample ids of vcf file as a vector of symbols for naming columns of num_array dataframe object for column filter functions
-"""
-@testset get_sample_names(reader) begin
-
end
-"""
- find_group_label_indices(pheno)
-find indices and determines names for group 1 and group 2 labels on plots. finds index of center of each sample group to place tick mark and label.
-"""
-@testset find_group_label_indices(pheno,trait_to_group_by,row_to_sort_by) begin
-end
-
-"""
- sortcols_by_phenotype_matrix(pheno_matrix_filename::String,trait_to_group_by::String,num_array::Array{Int64,2}, sample_names::Array{Symbol,2})
-group samples by a common trait using a user generated key matrix ("phenotype matrix")
-"""
-@testset sortcols_by_phenotype_matrix(pheno_matrix_filename::String,trait_to_group_by::String, num_array::Array{Int64,2}, sample_names::Array{Symbol,2}) begin
-
-end
-
-"""
- select_columns(filename_sample_list::AbstractString, num_array::Array{Int64,2}, sample_names::Array{Symbol,2})
-returns num_array with columns matching user generated list of sample ids to select for analysis. num_array now has sample ids in first row.
-"""
-@testset select_columns(filename_sample_list::AbstractString, num_array::Array{Int64,2}, sample_names::Array{Symbol,2}) begin
+@testset "avg_dp_variant" begin
+avg_variant_list=avg_dp_variant(dp_num_array)
+println("avg_dp_variant is $avg_variant_list")
end
+@testset "sortcols_by_phenotype_matrix" begin
+vcf,group_label_pack=sortcols_by_phenotype_matrix("test_files/sample_phenotype_matrix.csv","control,case", dp_num_array, sample_names)
+println(typeof(vcf))
+println(size(vcf,1))
+println(typeof(group_label_pack))
+println(length(group_label_pack))
+
+ @testset "find_group_label_indices" begin
+ pheno = readdlm("test_files/sample_phenotype_matrix.csv", ',')
+ row_to_sort_by = find(x -> x == "control,case", pheno)
+ row_to_sort_by = row_to_sort_by[1]
+ group_label_pack=find_group_label_indices(pheno,"control,case",row_to_sort_by)
+ println(typeof(group_label_pack))
+ println(length(group_label_pack))
+ end
-#functions for mathematic analysis
-"""
- avg_dp_samples(dp_num_array::Array{Int64,2})
-create sample_avg_list vector that lists averages of read depth for each sample for input into avg_sample_dp_line_chart(sample_avg_list)
-dp_num_array must contain dp values as Int64 and be without chromosome position columns
-"""
-@testset avg_dp_samples(dp_num_array::Array{Int64,2}) begin
+ @testset "select_columns" begin
+ dp_num_array=select_columns("test_files/select_samples_list.txt", dp_num_array, sample_names)
+ println(typeof(dp_num_array))
+ println(length(dp_num_array))
+ end
end
-
-
-"""
- avg_dp_variant(dp_num_array::Array{Int64,2})
-create variant_avg_list vector that lists averages of read depth for each variant for input into avg_variant_dp_line_chart(variant_avg_list)
-"""
-@testset avg_dp_variant(dp_num_array::Array{Int64,2}) begin
-
end
-
-"""
- list_sample_names_low_dp(sample_avg_list::Array{Float64,2},sample_names)
-returns list of sample ids that have an average read depth of under 15 across all variant positions
-"""
-@testset list_sample_names_low_dp(sample_avg_list::Array{Float64,1},sample_names) begin
-
end
"""
diff --git a/test/test_files/select_column_list.txt b/test/test_files/select_samples_list.txt
similarity index 100%
rename from test/test_files/select_column_list.txt
rename to test/test_files/select_samples_list.txt
diff --git a/viva_cli.jl b/viva_cli.jl
index 8209662..6171d20 100644
--- a/viva_cli.jl
+++ b/viva_cli.jl
@@ -268,6 +268,8 @@ if parsed_args["heatmap"] == "genotype"
graphic = ViVa.genotype_heatmap2(gt_num_array,title,chrom_label_info,sample_names)
end
+ println("saving now")
+
PlotlyJS.savefig(graphic, joinpath("$(parsed_args["output_directory"])" ,"$title.$(parsed_args["save_format"])"), js=:remote)
end
@@ -327,10 +329,7 @@ println("_______________________________________________")
if parsed_args["avg_dp"] == "sample"
if isdefined(:dp_num_array) == false
- read_depth_array = ViVa.generate_genotype_array(sub,"DP")
- clean_column1!(read_depth_array)
- read_depth_array=ViVa.sort_genotype_array(read_depth_array)
- dp_num_array,dp_chromosome_labels = translate_readdepth_strings_to_num_array(read_depth_array)
+ dp_num_array,dp_chromosome_labels=combined_all_read_depth_array_functions(sub)
end
chr_pos_tuple_list = generate_chromosome_positions_for_hover_labels(dp_chromosome_labels)
@@ -343,11 +342,9 @@ if parsed_args["avg_dp"] == "sample"
PlotlyJS.savefig(graphic, joinpath("$(parsed_args["output_directory"])" ,"Average Sample Read Depth.$(parsed_args["save_format"])"), js=:remote)
elseif parsed_args["avg_dp"] == "variant"
+
if isdefined(:dp_num_array) == false
- read_depth_array = ViVa.generate_genotype_array(sub,"DP")
- clean_column1!(read_depth_array)
- read_depth_array=ViVa.sort_genotype_array(read_depth_array)
- dp_num_array,dp_chromosome_labels = translate_readdepth_strings_to_num_array(read_depth_array)
+ dp_num_array,dp_chromosome_labels=combined_all_read_depth_array_functions(sub)
end
chr_pos_tuple_list = generate_chromosome_positions_for_hover_labels(dp_chromosome_labels)
From 22f2a8411c7fc84b982ddebe0860dca4549123a2 Mon Sep 17 00:00:00 2001
From: George Tollefson <gatollefson@gmail.com>
Date: Mon, 5 Nov 2018 14:20:45 -0500
Subject: [PATCH 2/6] Wrote all tests for test/new_vcf_utils. All are passing.
Fixed 4 sig list filter functions to iterate over VCF.Reader object first
then siglist to make faster. Allowed inputing vcf filename as path to
filename.
---
.gitignore | 1 +
.travis.yml | 35 ++--
ViVa_v2.jl | 15 --
open_jupyter_notebook.jl | 2 -
src/ViVa.jl | 8 +-
src/plot_utils.jl | 8 +-
src/vcf_utils_complete.jl | 142 ++++++++--------
test/.DS_Store | Bin 8196 -> 8196 bytes
test/new_vcf_utils.jl | 329 +++++++++++++++-----------------------
viva_cli.jl | 53 +++---
10 files changed, 255 insertions(+), 338 deletions(-)
delete mode 100644 ViVa_v2.jl
delete mode 100644 open_jupyter_notebook.jl
diff --git a/.gitignore b/.gitignore
index ea423ef..5f5d647 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,3 +5,4 @@
*.html
.DS_Store
.ipynb_checkpoints/
+output
diff --git a/.travis.yml b/.travis.yml
index df211b0..ddcbd6d 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,24 +1,23 @@
-## Documentation: http://docs.travis-ci.com/user/languages/julia/
language: julia
-# os:
-# - linux
-# - osx
-#
-# julia:
-# - 0.6
-#
-# notifications:
-# email: false
-#
-# git:
-# depth: 99999999
-#
-# before_script:
-# - export PATH=$HOME/.local/bin:$PATH
+os:
+ - linux
+ - osx
-# after_success:
-# - julia -e 'import Pkg; Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
+julia:
+ - 0.6
+
+notifications:
+ email: false
+
+git:
+ depth: 99999999
+
+before_script:
+ - export PATH=$HOME/.local/bin:$PATH
+
+after_success:
+ - julia -e 'Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
jobs:
include:
diff --git a/ViVa_v2.jl b/ViVa_v2.jl
deleted file mode 100644
index 9822dfa..0000000
--- a/ViVa_v2.jl
+++ /dev/null
@@ -1,15 +0,0 @@
-
-vcf_filename = "test_4X_191.vcf"
-field_to_visualize = "read_depth" # field(s) = "read_depth", *etc.
-variant_filter = ["range","chr4:0-4000000000"] #"range","chr4:0-4000000000"
-sample_filter = ["reorder_columns", "sample_phenotype_matrix.csv", "case_control_status"] # "select_columns", "select_column_list.txt",
-plot_types = "sample_line_chart"
-save_format = "html"
-plot_title = "Read_depth_test"
-
-
-using ViVa
-using GeneticVariation
-using VCFTools
-plot=ViVa.jupyter_main_new(vcf_filename,field_to_visualize,variant_filter,sample_filter,plot_types,save_format,plot_title)
-
diff --git a/open_jupyter_notebook.jl b/open_jupyter_notebook.jl
deleted file mode 100644
index bcac03b..0000000
--- a/open_jupyter_notebook.jl
+++ /dev/null
@@ -1,2 +0,0 @@
-using IJulia
-notebook()
diff --git a/src/ViVa.jl b/src/ViVa.jl
index be303b2..3e97735 100644
--- a/src/ViVa.jl
+++ b/src/ViVa.jl
@@ -1,13 +1,13 @@
module ViVa
-using DataFrames #use CSV.jl ? depwarnings
+using DataFrames
using PlotlyJS
using Rsvg
using Blink
-#using CSV
using GeneticVariation
using ArgParse
using VCFTools
+#using Base.Filesystem
@@ -42,9 +42,9 @@ export
avg_variant_dp_line_chart,
read_depth_threshhold,
list_variant_positions_low_dp,
- list_sample_positions_low_dp,
+ list_sample_names_low_dp,
avg_dp_variant,
- avg_dp_patients,
+ avg_dp_samples,
jupyter_main,
save_numerical_array,
io_pass_filter,
diff --git a/src/plot_utils.jl b/src/plot_utils.jl
index f86e74f..cdc7941 100644
--- a/src/plot_utils.jl
+++ b/src/plot_utils.jl
@@ -42,8 +42,8 @@ function genotype_heatmap2(input,title,chrom_label_info,sample_names)
end
"""
- genotype_heatmap_with_groups(input::Array{Int64,2},title::String,chrom_label_info::Tuple{Array{String,1},Array{Int64,1},String},group_label_pack::Array{Any,1},sample_names)
- generate heatmap of genotype data.
+ genotype_heatmap_with_groups(input::Array{Int64,2},title::String,chrom_label_info::Tuple{Array{String,1},Array{Int64,1},String},group_label_pack::Array{Any,1},sample_names)
+generate heatmap of genotype data.
"""
function genotype_heatmap_with_groups(input::Array{Int64,2},title::String,chrom_label_info::Tuple{Array{String,1},Array{Int64,1},String},group_label_pack::Array{Any,1},sample_names)
@@ -127,7 +127,7 @@ function dp_heatmap2(input, title, chrom_label_info, sample_names)
end
"""
- dp_heatmap2_with_groups(input::Array{Int64,2},title::String,chrom_label_info::Tuple{Array{String,1},Array{Int64,1},String},group_label_pack::Array{Any,1})
+ dp_heatmap2_with_groups(input::Array{Int64,2},title::String,chrom_label_info::Tuple{Array{String,1},Array{Int64,1},String},group_label_pack::Array{Any,1})
generate heatmap of read depth data with grouped samples.
"""
function dp_heatmap2_with_groups(input::Array{Int64,2},title::String,chrom_label_info::Tuple{Array{String,1},Array{Int64,1},String},group_label_pack::Array{Any,1})
@@ -174,7 +174,7 @@ function dp_heatmap2_with_groups(input::Array{Int64,2},title::String,chrom_label
end
"""
- avg_sample_dp_scatter(sample_avg_list::Array{Float64,1},sample_names)
+ avg_sample_dp_scatter(sample_avg_list::Array{Float64,1},sample_names)
generate line chart of average read depths of each sample.
"""
function avg_sample_dp_scatter(sample_avg_list::Array{Float64,1},sample_names)
diff --git a/src/vcf_utils_complete.jl b/src/vcf_utils_complete.jl
index fb8964e..de3b55a 100644
--- a/src/vcf_utils_complete.jl
+++ b/src/vcf_utils_complete.jl
@@ -110,42 +110,37 @@ end
io_sig_list_vcf_filter(sig_list,vcf_filename)
returns subarray of variant records matching a list of variant positions returned from load_siglist()
"""
-function io_sig_list_vcf_filter(sig_list,vcf_filename)
+function io_sig_list_vcf_filter(sig_list,vcf_filename)
- vcf_subarray = Array{Any}(0)
+ reader = VCF.Reader(open(vcf_filename, "r"))
- for row= 1:size(sig_list,1)
- dimension = size(sig_list,1)
+ vcf_subarray = Array{Any}(0)
- chr=(sig_list[row,1])
- pos=(sig_list[row,2])
+ for record in reader
- reader = VCF.Reader(open(vcf_filename, "r"))
- tic()
- for record in reader
+ for row= 1:size(sig_list,1)
+ dimension = size(sig_list,1)
- if typeof(VCF.chrom(record)) == String
- chr = string(chr)
- if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos)
- push!(vcf_subarray,record)
- end
+ chr=(sig_list[row,1])
+ pos=(sig_list[row,2])
+ if typeof(VCF.chrom(record)) == String
+ chr = string(chr)
+ if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos)
+ push!(vcf_subarray,record)
+ end
- end#remove this if need code below
-#=
- else
+ else
- if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos)
- push!(vcf_subarray,record)
+ if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos)
+ push!(vcf_subarray,record)
- end
- end
- =#
+ end
end
- toc()
- end
+ end
+ end
- return vcf_subarray
+ return vcf_subarray
end
"""
@@ -186,16 +181,16 @@ function pass_chrrange_siglist_filter(vcf_filename,sig_list,chr_range::AbstractS
vcf_subarray = Array{Any}(0)
- for row= 1:size(sig_list,1)
+ reader = VCF.Reader(open(vcf_filename, "r"))
+
+ for record in reader
+
+ for row = 1:size(sig_list,1)
dimension = size(sig_list,1)
chr=(sig_list[row,1])
pos=(sig_list[row,2])
- reader = VCF.Reader(open(vcf_filename, "r"))
-
- for record in reader
-
if typeof(VCF.chrom(record)) == String
chr = string(chr)
@@ -258,12 +253,16 @@ returns subarray of vcf records with io_pass_filter and io_chromosome_range_vcf_
end
"""
- pass_siglist_filter(vcf_filename,sig_list,chr_range::AbstractString)
- returns subarray of vcf records with io_pass_filter, io_sig_list_vcf_filter, and io_chromosome_range_vcf_filter applied.
+ pass_siglist_filter(vcf_filename,sig_list,chr_range::AbstractString)
+returns subarray of vcf records with io_pass_filter, io_sig_list_vcf_filter, and io_chromosome_range_vcf_filter applied.
"""
- function pass_siglist_filter(vcf_filename,sig_list)
+function pass_siglist_filter(vcf_filename,sig_list)
- vcf_subarray = Array{Any}(0)
+ vcf_subarray = Array{Any}(0)
+
+ reader = VCF.Reader(open(vcf_filename, "r"))
+
+ for record in reader
for row= 1:size(sig_list,1)
dimension = size(sig_list,1)
@@ -271,10 +270,6 @@ returns subarray of vcf records with io_pass_filter and io_chromosome_range_vcf_
chr=(sig_list[row,1])
pos=(sig_list[row,2])
- reader = VCF.Reader(open(vcf_filename, "r"))
-
- for record in reader
-
if typeof(VCF.chrom(record)) == String
chr = string(chr)
@@ -286,64 +281,63 @@ returns subarray of vcf records with io_pass_filter and io_chromosome_range_vcf_
if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos) && (VCF.hasfilter(record)) && (VCF.filter(record) == String["PASS"])
push!(vcf_subarray,record)
-
end
end
- end
end
+ end
- return vcf_subarray
- end
+ return vcf_subarray
+end
"""
chrrange_siglist_filter(vcf_filename,sig_list,chr_range::AbstractString)
returns subarray of vcf records with io_pass_filter, io_sig_list_vcf_filter, and io_chromosome_range_vcf_filter applied.
"""
- function chrrange_siglist_filter(vcf_filename,sig_list,chr_range::AbstractString)
+function chrrange_siglist_filter(vcf_filename,sig_list,chr_range::AbstractString)
- a=split(chr_range,":")
- chrwhole=a[1]
- chrnumber=split(chrwhole,"r")
- string_chr=chrnumber[2]
- chr=String(string_chr)
- range=a[2]
- splitrange=split(range, "-")
- lower_limit=splitrange[1]
- chr_range_low=parse(lower_limit)
- upper_limit=splitrange[2]
- chr_range_high=parse(upper_limit)
+ a=split(chr_range,":")
+ chrwhole=a[1]
+ chrnumber=split(chrwhole,"r")
+ string_chr=chrnumber[2]
+ chr=String(string_chr)
+ range=a[2]
+ splitrange=split(range, "-")
+ lower_limit=splitrange[1]
+ chr_range_low=parse(lower_limit)
+ upper_limit=splitrange[2]
+ chr_range_high=parse(upper_limit)
- vcf_subarray = Array{Any}(0)
+ vcf_subarray = Array{Any}(0)
- for row= 1:size(sig_list,1)
- dimension = size(sig_list,1)
+ reader = VCF.Reader(open(vcf_filename, "r"))
- chr=(sig_list[row,1])
- pos=(sig_list[row,2])
+ for record in reader
- reader = VCF.Reader(open(vcf_filename, "r"))
+ for row= 1:size(sig_list,1)
+ dimension = size(sig_list,1)
- for record in reader
+ chr=(sig_list[row,1])
+ pos=(sig_list[row,2])
- if typeof(VCF.chrom(record)) == String
- chr = string(chr)
+ if typeof(VCF.chrom(record)) == String
+ chr = string(chr)
- if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos) && ((VCF.chrom(record) == chr)) && ((chr_range_high > VCF.pos(record) > chr_range_low))
- push!(vcf_subarray,record)
- end
+ if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos) && ((VCF.chrom(record) == chr)) && ((chr_range_high > VCF.pos(record) > chr_range_low))
+ push!(vcf_subarray,record)
+ end
- else
+ else
- if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos) && ((VCF.chrom(record) == chr)) && ((chr_range_high > VCF.pos(record) > chr_range_low))
- push!(vcf_subarray,record)
+ if (VCF.chrom(record) == chr) && (VCF.pos(record) == pos) && ((VCF.chrom(record) == chr)) && ((chr_range_high > VCF.pos(record) > chr_range_low))
+ push!(vcf_subarray,record)
- end
- end
- end
+ end
+ end
end
+ end
- return vcf_subarray
- end
+ return vcf_subarray
+end
#functions for converting vcf record array to numerical array
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diff --git a/test/new_vcf_utils.jl b/test/new_vcf_utils.jl
index a0825e9..c1ee9fd 100644
--- a/test/new_vcf_utils.jl
+++ b/test/new_vcf_utils.jl
@@ -30,22 +30,24 @@ end
@testset "io_chromosome_range_vcf_filter" begin
sub = io_chromosome_range_vcf_filter("chr4:0-400000000",reader)
-println(sub[1:2])
-println(size(sub,2))
+@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))")
end
-#=
+
@testset "filters_with_siglist" begin
@testset "load_siglist" begin
sig_list=load_siglist("test_files/significantList_for_proteinstructures.csv")
- println(sig_list[2:1])
- println(size(sig_list,1))
+ #println(sig_list[2:1])
+ #println(size(sig_list,1))
@testset "clean_column1_siglist!" begin
clean_column1_siglist!(sig_list)
- println(sig_list[1,2])
- println(size(sig_list,1))
+ #println(sig_list[1,2])
+ #println(size(sig_list,1))
end
@testset "io_sig_list_vcf_filter" begin
@@ -75,7 +77,7 @@ end
end
end
-=#
+
@testset "io_pass_filter" begin
reader = VCF.Reader(open(vcf_filename, "r"))
@@ -98,237 +100,164 @@ reader = VCF.Reader(open(vcf_filename, "r"))
sub = io_pass_filter(reader)
gt_num_array,gt_chromosome_labels=combined_all_genotype_array_functions(sub)
-println(typeof(gt_num_array))
-println(length(gt_num_array))
-println(typeof(gt_chromosome_labels))
-println(length(gt_chromosome_labels))
+#println("combined_all_genotype_array_functions gt array is type: $(typeof(gt_num_array))")
+#println("combined_all_genotype_array_functions gt array is length: $(length(gt_num_array))")
+#println("combined_all_genotype_array_functions gt_chromosome_labels is typeof: $(typeof(gt_chromosome_labels))")
+#println("combined_all_genotype_array_functions gt_chromosome_labels is length: $(length(gt_chromosome_labels))")
+@test typeof(gt_num_array) == Array{Int64,2}
+@test length(gt_num_array) == 222324
+@test typeof(gt_chromosome_labels) == Array{Any,2}
+@test length(gt_chromosome_labels) == 2328
+
+ @testset "chromosome_label_generator" begin
+ chrom_label_info = ViVa.chromosome_label_generator(gt_chromosome_labels[:,1])
+ #println("chromosome_label_generator chrom_label_info is type $(typeof(chrom_label_info))")
+ #println("chromosome_label_generator chrom_label_info is length $(length(chrom_label_info))")
+ @test typeof(chrom_label_info) == Tuple{Array{String,1},Array{Int64,1},String}
+ @test size(chrom_label_info,1) == 3
+ end
+
+ @testset "generate_chromosome_positions_for_hover_labels" begin
+ chr_pos_tuple_list = generate_chromosome_positions_for_hover_labels(gt_chromosome_labels)
+ #println("generate_chromosome_positions_for_hover_labels chr_pos_tuple_list is type $(typeof(chr_pos_tuple_list))")
+ #println("generate_chromosome_positions_for_hover_labels chr_pos_tuple_list is length $(length(chr_pos_tuple_list))")
+ @test typeof(chr_pos_tuple_list) == Array{Tuple,1}
+ @test size(chr_pos_tuple_list,1) == 1164
+ end
@testset "generate_genotype_array" begin
reader = VCF.Reader(open(vcf_filename, "r"))
sub = io_pass_filter(reader)
genotype_array=generate_genotype_array(sub,"GT")
- println(typeof(genotype_array))
- println(length(genotype_array))
- println(genotype_array[3:5])
+
+ #println("generate_genotype_array is $(typeof(genotype_array))")
+ #println("generate_genotype_array is $(size(genotype_array,1))")
+ @test typeof(genotype_array) == Array{String,2}
+ @test size(genotype_array,1) == 1164
@testset "define_geno_dict" begin
geno_dict = define_geno_dict()
- println(typeof(geno_dict))
- println(length(geno_dict))
+ #println("define_geno_dict is type is $(typeof(geno_dict))")
+ #println("define_geno_dict is length is $(length(geno_dict))")
+ @test typeof(geno_dict) == Dict{Any,Any}
+ @test length(geno_dict) == 92
@testset "translate_genotype_to_num_array" begin
gt_num_array,gt_chromosome_labels=translate_genotype_to_num_array(genotype_array,geno_dict)
- println(typeof(gt_num_array))
- println(length(gt_num_array))
- println(typeof(gt_chromosome_labels))
- println(length(gt_chromosome_labels))
+ #println("translate_genotype_to_num_array gt_num_array type is $(typeof(gt_num_array))")
+ #println("translate_genotype_to_num_array gt_num_array length is $(length(gt_num_array))")
+ #println("translate_genotype_to_num_array gt_chromosome_labels typeof is $(typeof(gt_chromosome_labels))")
+ #println("translate_genotype_to_num_array gt_chromosome_labels length is $(length(gt_chromosome_labels))")
+ @test typeof(gt_num_array) == Array{Int64,2}
+ @test length(gt_num_array) == 222324
+ @test typeof(gt_chromosome_labels) == Array{String,2}
+ @test length(gt_chromosome_labels) == 2328
end
end
end
end
-@testset "combined_all_read_depth_array_functions" begin #inside functions same used in combined_all_genotype_array_functions
+@testset "combined_all_read_depth_array_functions" begin
reader = VCF.Reader(open(vcf_filename, "r"))
sub = io_pass_filter(reader)
dp_num_array,dp_chromosome_labels=combined_all_read_depth_array_functions(sub)
-println(typeof(dp_num_array))
-println(length(dp_num_array))
-println(typeof(dp_chromosome_labels))
-println(length(dp_chromosome_labels))
-
-@testset "get_sample_names" begin
-reader = VCF.Reader(open(vcf_filename, "r"))
-sample_names=get_sample_names(reader)
-println("get_sample_names")
-println(typeof(sample_names))
-println(length(sample_names))
-
-@testset "avg_dp_samples" begin
-avg_sample_list=avg_dp_samples(dp_num_array)
-println("avg_sample_list is $avg_sample_list")
-
-@testset "list_sample_names_low_dp" begin
-list=list_sample_names_low_dp(avg_sample_list,sample_names)
-println(list)
-end
-
-end
-
+#println("combined_all_read_depth_array_functions dp_num_array type is $(typeof(dp_num_array))")
+#println("combined_all_read_depth_array_functions dp_num_array length is $(length(dp_num_array))")
+#println("combined_all_read_depth_array_functions gt_chromosome_labels typeof is $(typeof(dp_chromosome_labels))")
+#println("combined_all_read_depth_array_functions gt_chromosome_labels length is $(length(dp_chromosome_labels))")
+@test typeof(dp_num_array) == Array{Int64,2}
+@test length(dp_num_array) == 222324
+@test typeof(dp_chromosome_labels) == Array{Any,2}
+@test length(dp_chromosome_labels) == 2328
-@testset "avg_dp_variant" begin
-avg_variant_list=avg_dp_variant(dp_num_array)
-println("avg_dp_variant is $avg_variant_list")
-end
+ @testset "get_sample_names" begin
+ reader = VCF.Reader(open(vcf_filename, "r"))
+ sample_names=get_sample_names(reader)
+ #println("get_sample_names")
+ #println("get_sample_names sample_names type is $(typeof(sample_names))")
+ #println("get_sample_names sample_names length is $(length(sample_names))")
+ @test typeof(sample_names) == Array{Symbol,2}
+ @test length(sample_names) == 191
+
+ @testset "read_depth_threshhold" begin
+ dp_num_array=read_depth_threshhold(dp_num_array)
+ #println("read_depth_threshhold dp_num_array is type $(typeof(dp_num_array))")
+ #println("read_depth_threshhold dp_num_array is size $(size(dp_num_array,1))")
+ @test typeof(dp_num_array) == Array{Int64,2}
+ @test size(dp_num_array,1) == 1164
+ end
-@testset "sortcols_by_phenotype_matrix" begin
-vcf,group_label_pack=sortcols_by_phenotype_matrix("test_files/sample_phenotype_matrix.csv","control,case", dp_num_array, sample_names)
-println(typeof(vcf))
-println(size(vcf,1))
-println(typeof(group_label_pack))
-println(length(group_label_pack))
-
- @testset "find_group_label_indices" begin
- pheno = readdlm("test_files/sample_phenotype_matrix.csv", ',')
- row_to_sort_by = find(x -> x == "control,case", pheno)
- row_to_sort_by = row_to_sort_by[1]
- group_label_pack=find_group_label_indices(pheno,"control,case",row_to_sort_by)
- println(typeof(group_label_pack))
- println(length(group_label_pack))
- end
+ @testset "avg_dp_samples" begin
+ avg_sample_list=avg_dp_samples(dp_num_array)
+ #println("avg_dp_samples avg_sample_list type is $(typeof(avg_sample_list))")
+ #println("avg_dp_samples avg_sample_list length is $(length(avg_sample_list))")
+ @test typeof(avg_sample_list) == Array{Float64,1}
+ @test size(avg_sample_list,1) == 191
+
+ @testset "list_sample_names_low_dp" begin
+ list=list_sample_names_low_dp(avg_sample_list,sample_names)
+ #println("list_sample_names_low_dp list type is $(typeof(list))")
+ #println("list_sample_names_low_dp list length is $(length(list))")
+ @test typeof(list) == Array{String,1}
+ @test size(list,1) == 6
+ end
- @testset "select_columns" begin
- dp_num_array=select_columns("test_files/select_samples_list.txt", dp_num_array, sample_names)
- println(typeof(dp_num_array))
- println(length(dp_num_array))
end
-end
-end
-end
-
-"""
- list_variant_positions_low_dp(variant_avg_list::Array{Float64,2},chrom_labels)
-finds variant positions that have an average read depth of under 15 across all patients
-"""
-function list_variant_positions_low_dp(variant_avg_list::Array{Float64,1},chrom_labels)
+ @testset "avg_dp_variant" begin
+ avg_variant_list=avg_dp_variant(dp_num_array)
+ #println("avg_dp_variant avg_variant_list type is $(typeof(avg_variant_list))")
+ #println("avg_dp_variant avg_variant_list length is $(length(avg_variant_list))")
+ @test typeof(avg_variant_list) == Array{Float64,1}
+ @test size(avg_variant_list,1) == 1164
- low_dp_index_list = Array{Int64}(0)
+ @testset "list_variant_positions_low_dp" begin
+ list=list_variant_positions_low_dp(avg_variant_list,dp_chromosome_labels)
+ #println("list_variant_positions_low_dp list type is $(typeof(list))")
+ #println("list_variant_positions_low_dp list length is $(length(list))")
+ @test typeof(list) == Array{Tuple{Int64,Int64},1}
+ @test size(list,1) == 33
- for item = 1:length(variant_avg_list)
- if variant_avg_list[item] < 15
- push!(low_dp_index_list,item)
- end
end
- low_dp_positions = Array{Tuple{Int64,Int64}}(0)
+ end
- for i in low_dp_index_list
- chrom_position = chrom_labels[i,1],chrom_labels[i,2]
- push!(low_dp_positions,chrom_position)
+ @testset "sortcols_by_phenotype_matrix" begin
+ vcf,group_label_pack=sortcols_by_phenotype_matrix("test_files/sample_phenotype_matrix.csv","control,case", 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))")
+ #println("sortcols_by_phenotype_matrix group_label_pack size is $(size(group_label_pack,1))")
+ @test typeof(vcf) == Array{Int64,2}
+ @test size(vcf,1) == 1164
+ @test typeof(group_label_pack) == Array{Any,1}
+ @test size(group_label_pack,1) == 5
+
+ @testset "find_group_label_indices" begin
+ pheno = readdlm("test_files/sample_phenotype_matrix.csv", ',')
+ row_to_sort_by = find(x -> x == "control,case", pheno)
+ row_to_sort_by = row_to_sort_by[1]
+ group_label_pack=find_group_label_indices(pheno,"control,case",row_to_sort_by)
+ #println("find_group_label_indices group_label_pack type is $(typeof(group_label_pack))")
+ #println("find_group_label_indices group_label_pack length is $(length(group_label_pack))")
+ @test typeof(group_label_pack) == Array{Any,1}
+ @test size(group_label_pack,1) == 5
end
- return low_dp_positions
-end
-
-#functions for producing objects for plot functions
-
-"""
- read_depth_threshhold(dp_array::Array{Int64,2})
-sets ceiling for read depth values at dp = 100. All dp over 100 are set to 100 to visualize read depth values between 0 < dp > 100 in better definition
-"""
-function read_depth_threshhold(dp_array::Array{Int64,2})
-
- dp_array[dp_array[:,:].>100].=100
-
- return dp_array
-end
-
-"""
- save_numerical_array(num_array::Matrix{Any},sample_names,chr_labels)
-save numerical array with chr labels and sample ids to working directory
-"""
-function save_numerical_array(num_array,sample_names,chr_labels)
-
- #samplenames=sample_names
- #samplenames=Matrix(samplenames)
-
- headings = hcat("chr","position")
- sample_names = hcat(headings,sample_names)
-
- chr_labeled_array_for_plotly=hcat(chr_labels, num_array)
- labeled_value_matrix_withsamplenames= vcat(sample_names,chr_labeled_array_for_plotly)
-
- writedlm("AC_gatk406_eh_PASS_withheader_value_matrix_.txt", labeled_value_matrix_withsamplenames, "\t")
-end
-
-"""
- chromosome_label_generator(chromosome_labels::Array{String,2})
-Returns vector of chr labels and indices to mark chromosomes in plotly heatmap
-Specifically, saves indexes and chrom labels in vectors to pass into heatmap function to ticvals and tictext respectively
-Input is either gt_chromosome_labels or dp_chromosome_labels from translate_gt/dp_to_num_array()
-"""
-
-function chromosome_label_generator(chromosome_labels::Array{Any,1})
- chrom_label_indices = findfirst.(map(a -> (y -> isequal(a, y)), unique(chromosome_labels)), [chromosome_labels])
- chrom_labels = unique(chromosome_labels)
- chrom_labels = [string(i) for i in chrom_labels]
-
- if length(chrom_labels) > 1
- for item=2:(length(chrom_labels))
-
- ratio=((chrom_label_indices[item])-(chrom_label_indices[item-1]))/(length(chromosome_labels))
- println(ratio)
-
- if ratio < 0.2
- font_size = "8"
- println("font size is $font_size")
- return chrom_labels,chrom_label_indices,font_size
- else
- font_size = "10"
- println("font size is $font_size")
-
- return chrom_labels,chrom_label_indices,font_size
- end
+ @testset "select_columns" begin
+ dp_num_array=select_columns("test_files/select_samples_list.txt", dp_num_array, sample_names)
+ #println("select_columns dp_num_array type is $(typeof(dp_num_array))")
+ #println("select_columns dp_num_array size is $(size(dp_num_array,1))")
+ @test typeof(dp_num_array) == Array{Int64,2}
+ @test size(dp_num_array,1) == 1164
end
- else
- font_size = "10"
- return chrom_labels,chrom_label_indices,font_size
end
-end
-"""
- checkfor_outputdirectory(path::String)
-Checks to see if output directory exists already. If it doesn't, it creates the new directory to write output files to.
-"""
-function checkfor_outputdirectory(path::String)
- if isdir(path) == true
- else
- mkdir(path)
end
-end
-
-"""
- generate_chromosome_positions_for_hover_labels(chr_labels::Array{Any,2})
-creates tuple of genomic locations to set as tick labels. This is automatically store chromosome positions in hover labels. However tick labels are set to hidden with showticklabels=false so they will not crowd the y axis.
-"""
-function generate_chromosome_positions_for_hover_labels(chr_labels::Array{Any,2})
-
-returnXY_column1!(chr_labels) #not working yet
-#println(chr_labels)
-
-chr_pos_tuple_list=Array{Tuple}(0)
-
- for row = 1:size(chr_labels,1)
-
- chr=chr_labels[row,1]
- pos=chr_labels[row,2]
- chr_pos_tuple=chr,pos
- push!(chr_pos_tuple_list,chr_pos_tuple)
end
- return chr_pos_tuple_list
-end
-
-"""
- returnXY_column1!(chr_label_vector)
-Replace String "23","24","25" with "X","Y","M" in chromosome label vector used for plot labels
-"""
-@testset "returnXY_column1!" begin
-
-end
-
-"""
- sort_genotype_array(genotype_array)
-sorts genotype array for GT or DP by chromosomal location
-"""
-@testset sort_genotype_array(genotype_array) begin
-
-end
-
-
-=#
end
diff --git a/viva_cli.jl b/viva_cli.jl
index 6171d20..6cfdd7a 100644
--- a/viva_cli.jl
+++ b/viva_cli.jl
@@ -1,8 +1,3 @@
-#=
-read_depth heatmap up to 15 white, up to 30 light blue,
-don't output files in same folder
-=#
-
println("Welcome to ViVa.")
println()
println("Loading packages:")
@@ -59,7 +54,7 @@ function test_parse_main(ARGS::Vector{String})
)
@add_arg_table s begin
- "--vcf_file", "-f" # vcf filename
+ "--vcf_file", "-f"
help = "vcf filename in format: file.vcf"
arg_type = String
required = true
@@ -73,7 +68,7 @@ function test_parse_main(ARGS::Vector{String})
arg_type = String
default = "output"
- "--save_format", "-s" # format to save graphics in
+ "--save_format", "-s"
help = "file format you wish to save graphics as (eg. pdf, html, png). Defaults to html"
arg_type = String
default = "html"
@@ -129,9 +124,7 @@ end
parsed_args = test_parse_main(ARGS)
-#begin main program
-
-#filter vcf and load matrix
+#filter vcf and load matrix of filtered vcf records
vcf_filename = (parsed_args["vcf_file"])
println("Reading $vcf_filename ...")
@@ -175,7 +168,7 @@ if parsed_args["show_stats"] == true
end
tic()
-
+#pass_filter
if parsed_args["pass_filter"] == true && parsed_args["chromosome_range"] == nothing && parsed_args["positions_list"] == nothing
sub = ViVa.io_pass_filter(reader)
number_rows = size(sub,1)
@@ -183,6 +176,7 @@ if parsed_args["pass_filter"] == true && parsed_args["chromosome_range"] == noth
heatmap_input = "pass_filtered"
end
+#chr_range
if parsed_args["chromosome_range"] != nothing && parsed_args["pass_filter"] == false && parsed_args["positions_list"] == nothing
sub = ViVa.io_chromosome_range_vcf_filter(parsed_args["chromosome_range"],reader)
number_rows = size(sub,1)
@@ -190,6 +184,7 @@ if parsed_args["chromosome_range"] != nothing && parsed_args["pass_filter"] == f
heatmap_input = "range_filtered"
end
+#list
if parsed_args["positions_list"] != nothing && parsed_args["chromosome_range"] == nothing && parsed_args["pass_filter"] == false
sig_list = load_siglist(parsed_args["positions_list"])
sub = ViVa.io_sig_list_vcf_filter(sig_list,vcf_filename)
@@ -198,6 +193,7 @@ if parsed_args["positions_list"] != nothing && parsed_args["chromosome_range"] =
heatmap_input = "positions_filtered"
end
+#pass_filter and chr_range and list
if parsed_args["pass_filter"] == true && parsed_args["chromosome_range"] != nothing && parsed_args["positions_list"] != nothing
sig_list = load_siglist(parsed_args["positions_list"])
sub = ViVa.pass_chrrange_siglist_filter(vcf_filename, sig_list, parsed_args["chromosome_range"])
@@ -205,12 +201,14 @@ if parsed_args["pass_filter"] == true && parsed_args["chromosome_range"] != noth
println("selected $number_rows variants with Filter status: PASS, that match list of chromosome positions of interest, and are within chromosome range: $(parsed_args["chromosome_range"])")
end
+#pass_filter and chr_range
if parsed_args["pass_filter"] == true && parsed_args["chromosome_range"] != nothing && parsed_args["positions_list"] == nothing
sub = ViVa.pass_chrrange_filter(reader, parsed_args["chromosome_range"])
number_rows = size(sub,1)
println("selected $number_rows variants with Filter status: PASS and are within chromosome range: $(parsed_args["chromosome_range"])")
end
+#pass_filter and list
if parsed_args["pass_filter"] == true && parsed_args["chromosome_range"] == nothing && parsed_args["positions_list"] != nothing
sig_list = load_siglist(parsed_args["positions_list"])
sub = ViVa.pass_siglist_filter(vcf_filename, sig_list)
@@ -218,6 +216,15 @@ if parsed_args["pass_filter"] == true && parsed_args["chromosome_range"] == noth
println("selected $number_rows variants with Filter status: PASS and that match list of chromosome positions of interest")
end
+#chr_range and list
+if parsed_args["pass_filter"] == false && parsed_args["chromosome_range"] != nothing && parsed_args["positions_list"] != nothing
+ sig_list = load_siglist(parsed_args["positions_list"])
+ sub = ViVa.chrrange_siglist_filter(vcf_filename, sig_list, parsed_args["chromosome_range"])
+ number_rows = size(sub,1)
+ println("selected $number_rows variants that are within chromosome range: $(parsed_args["chromosome_range"]) and that match list of chromosome positions of interest")
+end
+
+#no filters
if parsed_args["pass_filter"] == false && parsed_args["chromosome_range"] == nothing && parsed_args["positions_list"] == nothing
println("no filters applied. Large vcf files will take a long time to process and heatmap visualizations will lose resolution at this scale unless viewed in interactive html for zooming.")
@@ -232,13 +239,22 @@ if parsed_args["pass_filter"] == false && parsed_args["chromosome_range"] == not
end
+println()
+println("Finished Filtering. Total time to filter:")
+toc()
+println("_______________________________________________")
+
+#convert to numeric array for plotting and generate/save heatmaps and scatter plots
+
if parsed_args["heatmap"] == "genotype"
gt_num_array,gt_chromosome_labels = combined_all_genotype_array_functions(sub)
if parsed_args["heatmap_title"] != nothing
title = parsed_args["heatmap_title"]
else
- title = "Genotype_$(parsed_args["vcf_file"])"
+ bn = Base.Filesystem.basename(parsed_args["vcf_file"])
+ title = "Genotype_$bn"
+ println(title)
end
chr_pos_tuple_list = generate_chromosome_positions_for_hover_labels(gt_chromosome_labels)
@@ -249,7 +265,9 @@ if parsed_args["heatmap"] == "genotype"
if parsed_args["select_samples"] != nothing
println("selecting samples listed in $(parsed_args["select_samples"])")
- gt_num_array = select_columns(parsed_args["select_samples"], gt_num_array, sample_names)
+ gt_num_array = select_columns(parsed_args["select_samples"],
+ gt_num_array,
+ sample_names)
end
group_trait_matrix_filename=((parsed_args["group_samples"])[1])
@@ -319,13 +337,6 @@ if parsed_args["heatmap"] == "read_depth"
end
-#println("_______________________________________________")
-println()
-println("Finished Filtering. Total time to filter:")
-toc()
-println("_______________________________________________")
-#println()
-
if parsed_args["avg_dp"] == "sample"
if isdefined(:dp_num_array) == false
@@ -342,7 +353,7 @@ if parsed_args["avg_dp"] == "sample"
PlotlyJS.savefig(graphic, joinpath("$(parsed_args["output_directory"])" ,"Average Sample Read Depth.$(parsed_args["save_format"])"), js=:remote)
elseif parsed_args["avg_dp"] == "variant"
-
+
if isdefined(:dp_num_array) == false
dp_num_array,dp_chromosome_labels=combined_all_read_depth_array_functions(sub)
end
From 8c27f4ab3399b9e4d8c8a4ee3f3befeec7223f03 Mon Sep 17 00:00:00 2001
From: Fernando Gelin <fernando_gelin@brown.edu>
Date: Mon, 5 Nov 2018 14:33:19 -0500
Subject: [PATCH 3/6] Update .travis.yml
---
.travis.yml | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/.travis.yml b/.travis.yml
index ddcbd6d..fe06d90 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,7 +15,11 @@ git:
before_script:
- export PATH=$HOME/.local/bin:$PATH
-
+
+script:
+ - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
+ - julia --check-bounds=yes -e 'Pkg.clone(pwd()); Pkg.build("ViVa"); Pkg.test("ViVa"; coverage=true)'
+
after_success:
- julia -e 'Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
From 986b475e4daab2a8cdc13db36aba836e3f85d60f Mon Sep 17 00:00:00 2001
From: Fernando Gelin <fernando_gelin@brown.edu>
Date: Mon, 5 Nov 2018 14:46:26 -0500
Subject: [PATCH 4/6] Update .travis.yml
---
.travis.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.travis.yml b/.travis.yml
index fe06d90..9ca2b70 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,6 +15,7 @@ git:
before_script:
- export PATH=$HOME/.local/bin:$PATH
+ - julia -e 'Pkg.pin("Blink", v"0.6.2"); Pkg.pin("PlotlyJS", v"0.10.2"); Pkg.build("Blink")'
script:
- if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
From 77f4817fb0501401df8b4775b2939317b675bdc2 Mon Sep 17 00:00:00 2001
From: Fernando Gelin <fernando_gelin@brown.edu>
Date: Mon, 5 Nov 2018 14:52:27 -0500
Subject: [PATCH 5/6] Update .travis.yml
---
.travis.yml | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/.travis.yml b/.travis.yml
index 9ca2b70..0992315 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -15,11 +15,10 @@ git:
before_script:
- export PATH=$HOME/.local/bin:$PATH
- - julia -e 'Pkg.pin("Blink", v"0.6.2"); Pkg.pin("PlotlyJS", v"0.10.2"); Pkg.build("Blink")'
script:
- if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
- - julia --check-bounds=yes -e 'Pkg.clone(pwd()); Pkg.build("ViVa"); Pkg.test("ViVa"; coverage=true)'
+ - 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())'
From ff801a22b1ea62afb0e4de6c6c6826a6d1634ddc Mon Sep 17 00:00:00 2001
From: Fernando Gelin <fernando_gelin@brown.edu>
Date: Mon, 5 Nov 2018 15:15:41 -0500
Subject: [PATCH 6/6] Update ViVa.jl
---
src/ViVa.jl | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/ViVa.jl b/src/ViVa.jl
index 3e97735..8db9b81 100644
--- a/src/ViVa.jl
+++ b/src/ViVa.jl
@@ -6,7 +6,7 @@ using Rsvg
using Blink
using GeneticVariation
using ArgParse
-using VCFTools
+#using VCFTools
#using Base.Filesystem