tests/testthat/test-detect_paired.R

In alexvpickering/rkal: Run, Import, and Export 'kallisto' Quantifications

context("detect if samples are paired")

test_that("detect_paired identifies SRA fastq files", {

    fastq_id1s <- c('@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=72',
                    '@SRR001666.2 071112_SLXA-EAS1_s_7:5:1:801:338 length=72')

    expect_error(detect_paired(fastq_id1s), regexp = 'Please contact package author')

})


test_that("detect_paired handles older illumina sequence identifiers", {

    fastq_id1s <- c('@HWUSI-EAS100R:6:73:941:1973#0/1',
                    '@HWUSI-EAS100R:6:73:941:1973#0/1')

    expect_false(detect_paired(fastq_id1s))

})

test_that("detect_paired handles newer illumina sequence identifiers", {

    fastq_id1s <- c('@EAS139:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG',
                    '@EAS139:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG')

    expect_true(detect_paired(fastq_id1s))

})