minor edit

.gitignore

@@ -6,3 +6,4 @@
 **/.DS_Store
 /data
 /etc.
+/docs/Manifest.toml

README.md

@@ -17,7 +17,7 @@ using Pkg
 Pkg.activate(@__DIR__)
 Pkg.add(["GeneticsMakie", "CairoMakie", "Makie", "CSV", "DataFrames", "SnpArrays"])
 
-using GeneticsMakie, CairoMakie, Makie.GeometryBasics, CSV, DataFrames, SnpArrays, Statistics
+using GeneticsMakie, CairoMakie, Makie.GeometryBasics, CSV, DataFrames, SnpArrays, Statistics, Downloads
 
 const GM = GeneticsMakie
 CairoMakie.activate!(type = "png")
@@ -31,7 +31,7 @@ gencode = let
     url = "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/GRCh37_mapping/gencode.v39lift37.annotation.gtf.gz"
     file = basename(url)
     isdir("data/gencode") || mkdir("data/gencode")
-    isfile("data/gencode/$(file)") || download(url, "data/gencode/$(file)")
+    isfile("data/gencode/$(file)") || Downloads.download(url, "data/gencode/$(file)")
     h = ["seqnames", "source", "feature", "start", "end", "score", "strand", "phase", "info"]
     CSV.read("data/gencode/$(file)", DataFrame; delim = "\t", comment = "#", header = h)
 end
@@ -162,13 +162,13 @@ kgp = let
     url = joinpath(beagle, "b37.vcf/chr$(chr).1kg.phase3.v5a.vcf.gz")
     vcf = basename(url)
     isdir("data/1kg") || mkdir("data/1kg")
-    isfile("data/1kg/$(vcf)") || download(url, "data/1kg/$(vcf)")
+    isfile("data/1kg/$(vcf)") || Downloads.download(url, "data/1kg/$(vcf)")
     # Convert vcf file to plink bed file (this step takes a while)
     isfile("data/1kg/$(replace(vcf, ".vcf.gz" => ".bed"))") || vcf2plink("data/1kg/$(vcf)", "data/1kg/$(replace(vcf, ".vcf.gz" => ""))")
     # Download sample metadata
     url = joinpath(beagle, "sample_info/integrated_call_samples_v3.20130502.ALL.panel")
     meta = basename(url) 
-    isfile("data/1kg/$(meta)") || download(url, "data/1kg/$(meta)")
+    isfile("data/1kg/$(meta)") || Downloads.download(url, "data/1kg/$(meta)")
     # Subset data to the genomic region of interest and European samples
     kgp = SnpData("data/1kg/$(replace(vcf, ".vcf.gz" => ""))")
     meta = CSV.read("data/1kg/$(meta)", DataFrame)
@@ -244,7 +244,7 @@ gwas = let
         url = gwas[key][1]
         file = gwas[key][2]
         isdir("data/gwas") || mkdir("data/gwas")
-        isfile("data/gwas/$(file)") || download(url, "data/gwas/$(file)")
+        isfile("data/gwas/$(file)") || Downloads.download(url, "data/gwas/$(file)")
     end
     scz = CSV.read("data/gwas/$(gwas["scz"][2])", DataFrame; comment = "##", missingstring = ["NA"])
     bd = CSV.read("data/gwas/$(gwas["bd"][2])", DataFrame; comment = "##", missingstring = ["NA"])

docs/src/examples/gtf.md

@@ -12,12 +12,12 @@ the human genome (GRCh37), where we download the comprehensive
 gene annotation file in [GTF format](https://www.gencodegenes.org/pages/data_format.html).
 
 ```julia
-using GeneticsMakie, CSV, DataFrames
+using GeneticsMakie, CSV, DataFrames, Downloads
 isdir("data") || mkdir("data")
 url = "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/GRCh37_mapping/gencode.v39lift37.annotation.gtf.gz"
 file = basename(url)
 isdir("data/gencode") || mkdir("data/gencode")
-isfile("data/gencode/$(file)") || download(url, "data/gencode/$(file)")
+isfile("data/gencode/$(file)") || Downloads.download(url, "data/gencode/$(file)")
 h = ["seqnames", "source", "feature", "start", "end", "score", "strand", "phase", "info"]
 gencode = CSV.read("data/gencode/$(file)", DataFrame; delim = "\t", comment = "#", header = h)
 ```
@@ -54,4 +54,4 @@ GeneticsMakie.findgene("RBFOX1", gencode)
 
 !!! tip "Gene names"
     Make sure to use the correct gene name in case the gene cannot be found.
-    Gene names can be looked up in databases such as [GeneCards](https://www.genecards.org/).
+    The latest gene names can be looked up in databases such as [GeneCards](https://www.genecards.org/).

docs/src/examples/locus.md

@@ -51,19 +51,19 @@ Pkg.add("SnpArrays")
 ```
 
 ```julia
-using SnpArrays
+using SnpArrays, Downloads
 # Download 1000 Genomes data for a single chromosome
 beagle = "http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a"
 url = joinpath(beagle, "b37.vcf/chr$(chr).1kg.phase3.v5a.vcf.gz")
 vcf = basename(url)
 isdir("data/1kg") || mkdir("data/1kg")
-isfile("data/1kg/$(vcf)") || download(url, "data/1kg/$(vcf)")
+isfile("data/1kg/$(vcf)") || Downloads.download(url, "data/1kg/$(vcf)")
 # Convert vcf file to plink bed file (this step takes a while)
 isfile("data/1kg/$(replace(vcf, ".vcf.gz" => ".bed"))") || vcf2plink("data/1kg/$(vcf)", "data/1kg/$(replace(vcf, ".vcf.gz" => ""))")
 # Download sample metadata
 url = joinpath(beagle, "sample_info/integrated_call_samples_v3.20130502.ALL.panel")
 meta = basename(url) 
-isfile("data/1kg/$(meta)") || download(url, "data/1kg/$(meta)")
+isfile("data/1kg/$(meta)") || Downloads.download(url, "data/1kg/$(meta)")
 # Subset data to the genomic region of interest and European samples
 kgp = SnpData("data/1kg/$(replace(vcf, ".vcf.gz" => ""))")
 meta = CSV.read("data/1kg/$(meta)", DataFrame)

docs/src/examples/summary.md

@@ -9,7 +9,7 @@ Pkg.add(["GeneticsMakie", "CSV", "DataFrames"])
 ```
 
 ```julia
-using GeneticsMakie, CSV, DataFrames
+using GeneticsMakie, CSV, DataFrames, Downloads
 gwas = Dict(
     "height" => "https://portals.broadinstitute.org/collaboration/giant/images/6/63/Meta-analysis_Wood_et_al%2BUKBiobank_2018.txt.gz",
     "weight" => "https://portals.broadinstitute.org/collaboration/giant/images/c/c8/Meta-analysis_Locke_et_al%2BUKBiobank_2018_UPDATED.txt.gz"
@@ -18,7 +18,7 @@ isdir("data/gwas") || mkdir("data/gwas")
 df = DataFrame[]
 for key in keys(gwas)
     url = gwas[key]
-    isfile("data/gwas/$(basename(url))") || download(url, "data/gwas/$(basename(url))")
+    isfile("data/gwas/$(basename(url))") || Downloads.download(url, "data/gwas/$(basename(url))")
     push!(df, CSV.read("data/gwas/$(basename(url))", DataFrame; comment = "##", missingstring = ["NA"]))
 end
 ```

test/runtests.jl

@@ -1,7 +1,6 @@
 using GeneticsMakie
 using Test
 using CairoMakie
-using Makie.GeometryBasics
 using CSV
 using DataFrames
 using SnpArrays