tests/testthat/test-02_qc.R

In almeidasilvaf/GEAtlas: Building Expression Atlas from RNA-Seq data

#----Load data------------------------------------------------------------------
data(sample_info)

## Update PATH
Sys.setenv(
    PATH = paste(
        Sys.getenv("PATH"),
        "/opt/STAR-2.7.9a/bin/Linux_x86_64_static/",
        "/opt/bin/",
        "/opt/salmon-1.5.2_linux_x86_64/bin/",
        "/opt/kallisto/",
        "/opt/subread-2.0.3-Linux-x86_64/bin/",
        "/opt/stringtie-2.1.7.Linux_x86_64/",
        "/opt/taco-v0.7.3.Linux_x86_64/",
        sep = ":"
    )
)


#----Start tests----------------------------------------------------------------
test_that("get_fastq_paths() returns paths to FASTQ files", {
    
    fastqdir <- system.file("extdata", package = "bears")
    
    g1 <- get_fastq_paths(fastqdir, "SRR1039508", cmd = "P1")
    g2 <- get_fastq_paths(fastqdir, "SRR1039508", cmd = "P2")
    g3 <- get_fastq_paths(fastqdir, "SRR1039508", cmd = "S")
    g4 <- get_fastq_paths(fastqdir, "SRR1039509", cmd = "P1")
    g5 <- get_fastq_paths(fastqdir, "SRR1039509", cmd = "P2")
    
    expect_equal(class(g1), "character")    
    expect_equal(class(g2), "character")
    expect_null(g3)
    expect_null(g4)
    expect_null(g5)
})

test_that("summary_stats_star() returns a data frame of summary stats", {
    
    star_dir <- system.file("extdata", package = "bears")
    star_summary <- summary_stats_star(star_dir)
    
    expect_equal(class(star_summary), "data.frame")
    expect_equal(ncol(star_summary), 27)
})

test_that("summary_stats(fastp() returns a data frame of summary stats", {
    
    fastp_dir <- system.file("extdata", package = "bears")
    fastp_summary <- summary_stats_fastp(fastp_dir)
    
    expect_equal(class(fastp_summary), "data.frame")
    expect_equal(ncol(fastp_summary), 24)
})

test_that("summary_stats_salmon() returns a 2-column data frame", {
    
    salmondir <- system.file("extdata", package = "bears")
    biosamples <- "SAMN02422669"
    s <- summary_stats_salmon(salmondir, biosamples)
    
    expect_equal(class(s), "data.frame")
    expect_equal(ncol(s), 2)
    
})