test_seq <- c(seq1 = "AAAAAAAAAAGGGGGGGGGGTTTTTTTTTTCCCCCCCCCC")
test_pos <- tibble::tibble(
seq_id = rep("seq1", 4),
region = LETTERS[1:4],
start = c(1L, 11L, 21L, 31L),
end = c(10L, 20L, 30L, 40L)
)
test_result <- c(seq1 = "TTTTTTTTTT")
test_ShortRead <- methods::as(test_seq, "ShortRead")
test_DNAStringSet <- Biostrings::DNAStringSet(test_seq)
test_RNAStringSet <- Biostrings::RNAStringSet(test_DNAStringSet)
test_fasta <- tempfile("test", fileext = ".fasta.gz")
Biostrings::writeXStringSet(test_DNAStringSet, test_fasta, compress = TRUE)
test_outfasta <- tempfile("test", fileext = ".fasta.gz")
extract_region(test_fasta, test_pos, region = "C", outfile = test_outfasta)
test_qual <- rep(10L, nchar(test_seq))
test_QualityScaledDNAStringSet <- Biostrings::QualityScaledDNAStringSet(
test_DNAStringSet,
Biostrings::PhredQuality(test_qual)
)
test_QualityScaledRNAStringSet <- Biostrings::QualityScaledRNAStringSet(
test_RNAStringSet,
Biostrings::PhredQuality(test_qual)
)
test_ShortReadQ <- methods::as(test_QualityScaledDNAStringSet, "ShortReadQ")
test_fastq <- tempfile("test", fileext = ".fastq.gz")
Biostrings::writeQualityScaledXStringSet(test_QualityScaledDNAStringSet, test_fastq)
test_outfastq <- tempfile("test", fileext = ".fastq.gz")
extract_region(test_fastq, test_pos, region = "C", outfile = test_outfastq)
test_that("extract_regions works for all formats", {
expect_identical(
extract_region(test_seq, test_pos, region = "C"),
test_result
)
expect_equal(
methods::as(
extract_region(test_ShortRead, test_pos, region = "C"),
"character"
),
test_result
)
expect_equal(
methods::as(
extract_region(test_DNAStringSet, test_pos, region = "C"),
"character"
),
test_result
)
expect_equal(
methods::as(
extract_region(test_RNAStringSet, test_pos, region = "C"),
"character"
),
chartr("T", "U", test_result)
)
expect_equal(
methods::as(
extract_region(test_ShortReadQ, test_pos, region = "C"),
"character"
),
test_result
)
expect_equal(
methods::as(
extract_region(test_QualityScaledDNAStringSet, test_pos, region = "C"),
"character"
),
test_result
)
expect_equal(
methods::as(
extract_region(test_QualityScaledRNAStringSet, test_pos, region = "C"),
"character"
),
chartr("T", "U", test_result)
)
expect_equal(
methods::as(
Biostrings::readDNAStringSet(test_outfasta),
"character"
),
test_result
)
})
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