context("read_population.R")
test_that("error checking", {
path <- system.file("extdata","data_2_column.csv",package="gstudio")
# normal data.frame w/o genetic dta
expect_that( data <- read.population(path), throws_error() )
# bad locus.columns
expect_that( (data <- read.population(path, locus.columns="BOB")), throws_error() )
# wrong value for locus.columns
expect_that( (data <- read.population(path, locus.columns=2:40)), throws_error() )
})
test_that("two column file", {
path <- system.file("extdata","data_2_column.csv",package="gstudio")
# self-correcting locus.column
data <- read_population( path, type="column", locus.columns=4:7)
expect_that( data, is_a("data.frame"))
expect_that( length(column_class(data,"locus")), equals(2) )
# propertly specified locus.column
data <- read_population( path, type="column", locus.columns=seq(4,7,by=2))
expect_that( data, is_a("data.frame") )
expect_that( length(column_class(data,"locus")), equals(2) )
})
test_that("reading aflp data file",{
path <- system.file("extdata","data_aflp.csv",package="gstudio")
data <- read_population(path, type="aflp", locus.columns=4:7)
expect_that( data, is_a("data.frame") )
expect_that( length( column_class(data,"locus")), equals(4) )
})
test_that("reading separated data file",{
path <- system.file("extdata","data_separated.csv",package="gstudio")
data <- read_population(path, type="separated", locus.columns=4:5, delim=":" )
expect_that( data, is_a("data.frame") )
expect_that( length( column_class(data,"locus")), equals(2) )
})
test_that("reading snp data file",{
path <- system.file("extdata","data_snp.csv",package="gstudio")
data <- read_population(path,type="snp",locus.columns=4:7 )
expect_that( data, is_a("data.frame") )
expect_that( length( column_class(data,"locus")), equals(4) )
})
test_that("reading zyme data file",{
path <- system.file("extdata","data_zymelike.csv",package="gstudio")
data <- read_population(path, type="zyme",locus.columns=4:7 )
expect_that( data, is_a("data.frame") )
expect_that( length( column_class(data,"locus")), equals(4) )
})
test_that("reading structure data file", {
path <- system.file("extdata","data_structure.str", package="gstudio")
data <- read_population(path, type="structure")
expect_that( data, is_a("data.frame") )
expect_that( length(column_class(data,"locus")), equals(15) )
})
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