longtests/testthat/test-makeGRangesFromGff.R
In acidgenomics/AcidGenomes: Acid Genomics Genome Annotations
test_that("Unsupported files", {
for (file in gffs[c(
"flybase_gff3",
"wormbase_gff3"
)]) {
expect_error(
object = makeGRangesFromGff(file = file),
regexp = "isSupportedGFF"
)
}
})
file <- gffs[["ensembl_grch38_gff3"]]
test_that("GFF3 genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = FALSE
)
expect_s4_class(object, "EnsemblGenes")
expect_length(object, 62703L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"logicName" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "CompressedCharacterList",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000116044.17"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "2",
"start" = "177218667",
"end" = "177392756",
"width" = "174090",
"strand" = "-",
"broadClass" = "coding",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"logicName" = "ensembl_havana_gene_homo_sapiens",
"ncbiGeneId" = "4780",
"source" = "ensembl_havana",
"tag" = "character(0)",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object))[seq_len(25L)],
expected = c(
"1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y", "MT"
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["1", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38.p13"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38.p13"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "0d9311600fa404a31f517b752002dcda"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
expect_identical(
object = metadata(object)[["release"]],
expected = 108L
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "4cf5bfc008e3a9b8d22d7613d989ee72dd7424dca552ce14cc3d5a87e0ca8048" # nolint
)
})
test_that("GFF3 transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "EnsemblTranscripts")
expect_length(object, 252300L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"logicName" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "CompressedCharacterList",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdNoVersion" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000397062.8"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "2",
"start" = "177230308",
"end" = "177264727",
"width" = "34420",
"strand" = "-",
"broadClass" = "coding",
"ccdsId" = "CCDS42782.1",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"logicName" = "ensembl_havana_gene_homo_sapiens",
"ncbiGeneId" = "4780",
"source" = "ensembl_havana",
"tag" = "c(\"basic\", \"Ensembl_canonical\", \"MANE_Select\")",
"txBiotype" = "protein_coding",
"txId" = "ENST00000397062.8",
"txIdNoVersion" = "ENST00000397062",
"txIdVersion" = "ENST00000397062.8",
"txName" = "NFE2L2-201",
"txSupportLevel" = "1 (assigned to previous version 7)",
"type" = "mRNA"
)
)
})
file <- gffs[["ensembl_grch38_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = FALSE
)
expect_s4_class(object, "EnsemblGenes")
expect_length(object, 62703L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000116044.17"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "2",
"start" = "177218667",
"end" = "177392756",
"width" = "174090",
"strand" = "-",
"broadClass" = "coding",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSource" = "ensembl_havana",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"ncbiGeneId" = "4780",
"source" = "ensembl_havana",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object))[seq_len(25L)],
expected = c(
"1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y", "MT"
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["1", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38.p13"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38.p13"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "27864327a647f9fdae2cafff5f3ea45e"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
expect_identical(
object = metadata(object)[["release"]],
expected = 108L
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "1ae26267acf522d8d9a94736e2c00b5ff1008d43623fc73644092016ae0c57e8" # nolint
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "EnsemblTranscripts")
expect_length(object, 252301L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdNoVersion" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSource" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000397062.8"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "2",
"start" = "177230308",
"end" = "177264727",
"width" = "34420",
"strand" = "-",
"broadClass" = "coding",
"ccdsId" = "CCDS42782",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSource" = "ensembl_havana",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"ncbiGeneId" = "4780",
"source" = "ensembl_havana",
"tag" = "MANE_Select",
"txBiotype" = "protein_coding",
"txId" = "ENST00000397062.8",
"txIdNoVersion" = "ENST00000397062",
"txIdVersion" = "ENST00000397062.8",
"txName" = "NFE2L2-201",
"txSource" = "ensembl_havana",
"txSupportLevel" = "1 (assigned to previous version 7)",
"type" = "transcript"
)
)
})
file <- gffs[["flybase_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes"
)
expect_s4_class(object, "FlybaseGenes")
expect_length(object, 17896L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["FBgn0262975"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "3R",
"start" = "23185580",
"end" = "23226711",
"width" = "41132",
"strand" = "-",
"broadClass" = "other",
"geneId" = "FBgn0262975",
"geneName" = "cnc",
"source" = "FlyBase",
"type" = "gene"
)
)
expect_true(isSubset(
x = c(
"2L", "2R", "3L", "3R", "4", "X", "Y",
"mitochondrion_genome", "rDNA"
),
y = levels(seqnames(object))
))
expect_true(all(is.na(seqlengths(object))))
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "r6.49"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "722ba353d2dd6d3036d747f1498a2e9f"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Drosophila melanogaster"
)
expect_identical(
object = metadata(object)[["release"]],
expected = "r6.49"
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "565b486cbfe78942127482018e4439a28a6b171d71624d8ffe2a3611e162a101" # nolint
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts"
)
expect_s4_class(object, "FlybaseTranscripts")
expect_length(object, 35723L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"source" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["FBtr0306744"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "3R",
"start" = "23185580",
"end" = "23191120",
"width" = "5541",
"strand" = "-",
"broadClass" = "other",
"geneId" = "FBgn0262975",
"geneName" = "cnc",
"source" = "FlyBase",
"txId" = "FBtr0306744",
"txName" = "cnc-RF",
"type" = "mRNA"
)
)
})
file <- gffs[["gencode_grch38_gff3"]]
test_that("GFF3 genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = FALSE
)
expect_s4_class(object, "GencodeGenes")
expect_length(object, 62696L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"artifDupl" = "Rle",
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"havanaGene" = "Rle",
"hgncId" = "Rle",
"level" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "CompressedCharacterList",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000116044.17"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr2",
"start" = "177218667",
"end" = "177392756",
"width" = "174090",
"strand" = "-",
"artifDupl" = NA_character_,
"broadClass" = "coding",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"havanaGene" = "OTTHUMG00000133620.18",
"hgncId" = "HGNC:7782",
"level" = "1",
"ncbiGeneId" = "4780",
"source" = "HAVANA",
"tag" = "c(\"ncRNA_host\", \"overlapping_locus\")",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object)),
expected = paste0(
"chr",
c(
seq(from = 1L, to = 22L),
"X", "Y", "M"
)
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["chr1", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "b0199f8b1522f61093896e8d48750a0c"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
expect_identical(
object = metadata(object)[["release"]],
expected = 42L
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "10d01b26b75d0142677d0bddf369af375c2e24f6b4c99ce04f408032c51ca432" # nolint
)
})
test_that("GFF3 transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "GencodeTranscripts")
expect_length(object, 252416L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"havanaGene" = "Rle",
"havanaTranscript" = "Rle",
"hgncId" = "Rle",
"level" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"proteinId" = "Rle",
"source" = "Rle",
"tag" = "CompressedCharacterList",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdNoVersion" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000397062.8"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr2",
"start" = "177230308",
"end" = "177264727",
"width" = "34420",
"strand" = "-",
"broadClass" = "coding",
"ccdsId" = "CCDS42782.1",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"havanaGene" = "OTTHUMG00000133620.18",
"havanaTranscript" = "OTTHUMT00000257752.5",
"hgncId" = "HGNC:7782",
"level" = "2",
"ncbiGeneId" = "4780",
"proteinId" = "ENSP00000380252.3",
"source" = "HAVANA",
"tag" = paste(
"c(\"basic\",",
"\"Ensembl_canonical\",",
"\"MANE_Select\",",
"\"appris_alternative_1\",",
"\"CCDS\")"
),
"txBiotype" = "protein_coding",
"txId" = "ENST00000397062.8",
"txIdNoVersion" = "ENST00000397062",
"txIdVersion" = "ENST00000397062.8",
"txName" = "NFE2L2-201",
"txSupportLevel" = "1",
"type" = "transcript"
)
)
})
file <- gffs[["gencode_grch38_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = FALSE
)
expect_s4_class(object, "GencodeGenes")
expect_length(object, 62696L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"artifDupl" = "Rle",
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"havanaGene" = "Rle",
"hgncId" = "Rle",
"level" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000116044.17"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr2",
"start" = "177218667",
"end" = "177392756",
"width" = "174090",
"strand" = "-",
"artifDupl" = NA_character_,
"broadClass" = "coding",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"havanaGene" = "OTTHUMG00000133620.18",
"hgncId" = "HGNC:7782",
"level" = "1",
"ncbiGeneId" = "4780",
"source" = "HAVANA",
"tag" = "overlapping_locus",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object)),
expected = paste0(
"chr",
c(
seq(from = 1L, to = 22L),
"X", "Y", "M"
)
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["chr1", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "b3a1bb9b1239d8075dd2b031817a36da"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
expect_identical(
object = metadata(object)[["release"]],
expected = 42L
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "f59a5b38c6de1472430ccd0181927a01df0b4ad8d78f598e521badc9da80a76e" # nolint
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "GencodeTranscripts")
expect_length(object, 252416L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"havanaGene" = "Rle",
"havanaTranscript" = "Rle",
"hgncId" = "Rle",
"level" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"proteinId" = "Rle",
"source" = "Rle",
"tag" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdNoVersion" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000397062.8"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr2",
"start" = "177230308",
"end" = "177264727",
"width" = "34420",
"strand" = "-",
"broadClass" = "coding",
"ccdsId" = "CCDS42782.1",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"havanaGene" = "OTTHUMG00000133620.18",
"havanaTranscript" = "OTTHUMT00000257752.5",
"hgncId" = "HGNC:7782",
"level" = "2",
"ncbiGeneId" = "4780",
"proteinId" = "ENSP00000380252.3",
"source" = "HAVANA",
"tag" = "CCDS",
"txBiotype" = "protein_coding",
"txId" = "ENST00000397062.8",
"txIdNoVersion" = "ENST00000397062",
"txIdVersion" = "ENST00000397062.8",
"txName" = "NFE2L2-201",
"txSupportLevel" = "1",
"type" = "transcript"
)
)
})
file <- gffs[["refseq_grch38_gff3"]]
test_that("GFF3 genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes"
)
expect_s4_class(object, "RefseqGenes")
expect_identical(
object = lapply(mcols(object[[1L]]), simpleClass),
expected = list(
"broadClass" = "Rle",
"dbxref" = "CompressedCharacterList",
"description" = "Rle",
"exception" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSynonym" = "CompressedCharacterList",
"ncbiGeneId" = "Rle",
"parentGeneId" = "Rle",
"partial" = "Rle",
"pseudo" = "Rle",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = lapply(
X = as.data.frame(object[["AATF"]]),
FUN = as.character
),
expected = list(
"seqnames" = c("NC_000017.11", "NT_187614.1"),
"start" = c("36948954", "1185319"),
"end" = c("37056871", "1293236"),
"width" = rep("107918", 2L),
"strand" = rep("+", 2L),
"broadClass" = rep("coding", 2L),
"dbxref" = c(
"c(\"GeneID:26574\", \"HGNC:HGNC:19235\", \"MIM:608463\")",
"c(\"GeneID:26574\", \"HGNC:HGNC:19235\", \"MIM:608463\")"
),
"description" =
rep("apoptosis antagonizing transcription factor", 2L),
"exception" = rep(NA_character_, 2L),
"geneBiotype" = rep("protein_coding", 2L),
"geneId" = rep("AATF", 2L),
"geneName" = rep("AATF", 2L),
"geneSynonym" =
rep("c(\"BFR2\", \"CHE-1\", \"CHE1\", \"DED\")", 2L),
"ncbiGeneId" = rep("26574", 2L),
"parentGeneId" = c("AATF", "AATF-2"),
"partial" = rep(NA_character_, 2L),
"pseudo" = rep(NA_character_, 2L),
"source" = c("BestRefSeq%2CGnomon", "BestRefSeq%2CGnomon"),
"type" = rep("gene", 2L)
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["NC_000001.11", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38.p14"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38.p14"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
})
test_that("GFF3 transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts"
)
expect_s4_class(object, "RefseqTranscripts")
expect_true(all(grepl(
pattern = "^[A-Z]{2}_[0-9]+\\.[0-9]+$",
x = names(object)
)))
expect_identical(
object = lapply(mcols(object[[1L]]), simpleClass),
expected = list(
"broadClass" = "Rle",
"dbxref" = "CompressedCharacterList",
"description" = "Rle",
"exception" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSynonym" = "CompressedCharacterList",
"inference" = "Rle",
"modelEvidence" = "Rle",
"ncbiGeneId" = "Rle",
"parentGeneId" = "Rle",
"partial" = "Rle",
"product" = "Rle",
"pseudo" = "Rle",
"source" = "Rle",
"tag" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object[["NM_000014.6"]]),
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "NC_000012.12",
"start" = "9067708",
"end" = "9115919",
"width" = "48212",
"strand" = "-",
"broadClass" = "coding",
"dbxref" = paste(
"c(\"Ensembl:ENST00000318602.12\",",
"\"GeneID:2\",",
"\"GenBank:NM_000014.6\",",
"\"HGNC:HGNC:7\",",
"\"MIM:103950\")"
),
"description" = "alpha-2-macroglobulin",
"exception" = NA_character_,
"geneBiotype" = "protein_coding",
"geneId" = "A2M",
"geneName" = "A2M",
"geneSynonym" = "character(0)",
"inference" = NA_character_,
"modelEvidence" = NA_character_,
"ncbiGeneId" = "2",
"parentGeneId" = "A2M",
"partial" = NA_character_,
"product" = "alpha-2-macroglobulin, transcript variant 1",
"pseudo" = NA_character_,
"source" = "BestRefSeq",
"tag" = "MANE Select",
"txId" = "NM_000014.6",
"txName" = "NM_000014.6",
"type" = "mRNA"
)
)
})
file <- gffs[["refseq_grch38_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes"
)
expect_s4_class(object, "RefseqGenes")
expect_identical(
object = lapply(mcols(object[[1L]]), simpleClass),
expected = list(
"broadClass" = "Rle",
"dbXref" = "Rle",
"description" = "Rle",
"exception" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSynonym" = "Rle",
"ncbiGeneId" = "Rle",
"parentGeneId" = "Rle",
"partial" = "Rle",
"pseudo" = "Rle",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = lapply(
X = as.data.frame(object[["AATF"]]),
FUN = as.character
),
expected = list(
"seqnames" = c("NC_000017.11", "NT_187614.1"),
"start" = c("36948954", "1185319"),
"end" = c("37056871", "1293236"),
"width" = rep("107918", 2L),
"strand" = rep("+", 2L),
"broadClass" = rep("coding", 2L),
"dbXref" = rep("MIM:608463", 2L),
"description" =
rep("apoptosis antagonizing transcription factor", 2L),
"exception" = rep(NA_character_, 2L),
"geneBiotype" = rep("protein_coding", 2L),
"geneId" = rep("AATF", 2L),
"geneName" = rep("AATF", 2L),
"geneSynonym" = rep("DED", 2L),
"ncbiGeneId" = rep("26574", 2L),
"parentGeneId" = c("AATF", "AATF_1"),
"partial" = rep(NA_character_, 2L),
"pseudo" = rep(NA_character_, 2L),
"source" = c("BestRefSeq%2CGnomon", "BestRefSeq%2CGnomon"),
"type" = rep("gene", 2L)
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["NC_000001.11", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38.p14"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38.p14"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts"
)
expect_s4_class(object, "RefseqTranscripts")
expect_true(all(grepl(
pattern = "^[A-Z]{2}_[0-9]+\\.[0-9]+$",
x = names(object)
)))
expect_identical(
object = lapply(mcols(object[[1L]]), simpleClass),
expected = list(
"broadClass" = "Rle",
"dbXref" = "Rle",
"description" = "Rle",
"exception" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"inference" = "Rle",
"modelEvidence" = "Rle",
"ncbiGeneId" = "Rle",
"parentGeneId" = "Rle",
"partial" = "Rle",
"product" = "Rle",
"pseudo" = "Rle",
"source" = "Rle",
"tag" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object[["NM_000014.6"]]),
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "NC_000012.12",
"start" = "9067708",
"end" = "9115919",
"width" = "48212",
"strand" = "-",
"broadClass" = "coding",
"dbXref" = "GeneID:2",
"description" = "alpha-2-macroglobulin",
"exception" = NA_character_,
"geneBiotype" = "protein_coding",
"geneId" = "A2M",
"geneName" = "A2M",
"inference" = NA_character_,
"modelEvidence" = NA_character_,
"ncbiGeneId" = "2",
"parentGeneId" = "A2M",
"partial" = NA_character_,
"product" = "alpha-2-macroglobulin, transcript variant 1",
"pseudo" = NA_character_,
"source" = "BestRefSeq",
"tag" = "MANE Select",
"txBiotype" = "mRNA",
"txId" = "NM_000014.6",
"txName" = "NM_000014.6",
"type" = "transcript"
)
)
})
file <- gffs[["ucsc_hg38_ncbirefseq_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = TRUE
)
expect_s4_class(object, "UcscGenes")
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"geneId" = "Rle",
"geneName" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["A1BG"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr19",
"start" = "58345183",
"end" = "58353492",
"width" = "8310",
"strand" = "-",
"geneId" = "A1BG",
"geneName" = "A1BG"
)
)
## UCSC has changed some things related to hg38 that is currently causing
## issues with GenomeInfoDb (v1.34.7).
## https://github.com/Bioconductor/GenomeInfoDb/issues/83
## > expect_identical(
## > object = as.data.frame(seqinfo(object))["chr1", , drop = TRUE],
## > expected = list(
## > "seqlengths" = 248956422L,
## > "isCircular" = FALSE,
## > "genome" = "hg38"
## > )
## > )
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "hg38"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "UcscTranscripts")
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"geneId" = "Rle",
"geneName" = "Rle",
"txBiotype" = "Rle",
"txChrom" = "Rle",
"txEnd" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"txNumber" = "Rle",
"txStart" = "Rle",
"txStrand" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ABCA3P1_2"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr16",
"start" = "21938865",
"end" = "21940466",
"width" = "1602",
"strand" = "+",
"geneId" = "ABCA3P1",
"geneName" = "ABCA3P1",
"txBiotype" = "transcript",
"txChrom" = "chr16",
"txEnd" = "21940466",
"txId" = "ABCA3P1_2",
"txName" = "ABCA3P1_2",
"txNumber" = "144018",
"txStart" = "21938865",
"txStrand" = "+"
)
)
})
file <- gffs[["wormbase_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes"
)
expect_s4_class(object, "WormbaseGenes")
expect_length(object, 46928L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneVersion" = "Rle",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["WBGene00022276"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "I",
"start" = "11495",
"end" = "16837",
"width" = "5343",
"strand" = "+",
"broadClass" = "coding",
"geneBiotype" = "protein_coding",
"geneId" = "WBGene00022276",
"geneName" = "nlp-40",
"geneSource" = "WormBase",
"geneVersion" = "1",
"source" = "WormBase",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object)),
expected = c(
"I",
"II",
"III",
"IV",
"V",
"X",
"MtDNA"
)
)
expect_true(all(is.na(seqlengths(object))))
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "WS287"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "5c45625e18ee2b5d4b9830da34cd01bf"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Caenorhabditis elegans"
)
expect_identical(
object = metadata(object)[["release"]],
expected = "WS287"
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "6b8756bd1dfd5995e0c242d35bf3b3d3b04208a65cbf16bc7bfb9befb9a3684f" # nolint
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts"
)
expect_s4_class(object, "WormbaseTranscripts")
expect_length(object, 60136L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneVersion" = "Rle",
"source" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"txSource" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["Y74C9A.2a.3"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "I",
"start" = "11495",
"end" = "16793",
"width" = "5299",
"strand" = "+",
"broadClass" = "coding",
"geneBiotype" = "protein_coding",
"geneId" = "WBGene00022276",
"geneName" = "nlp-40",
"geneSource" = "WormBase",
"geneVersion" = "1",
"source" = "WormBase",
"txBiotype" = "protein_coding",
"txId" = "Y74C9A.2a.3",
"txName" = "Y74C9A.2a.3",
"txSource" = "WormBase",
"type" = "transcript"
)
)
})
file <- file.path(cacheDir, "ref-transcripts.gtf")
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = TRUE
)
expect_s4_class(object, "EnsemblGenes")
expect_length(object, n = 60L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000284332"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr1",
"start" = "30366",
"end" = "30503",
"width" = "138",
"strand" = "+",
"broadClass" = "small",
"description" = paste(
"microRNA 1302-2",
"[Source:HGNC Symbol;Acc:HGNC:35294]"
),
"geneBiotype" = "miRNA",
"geneId" = "ENSG00000284332",
"geneIdVersion" = "ENSG00000284332.1",
"geneName" = "MIR1302-2",
"geneSource" = "mirbase",
"geneSynonyms" = "c(\"HSA-MIR-1302-2\", \"MIRN1302-2\")",
"ncbiGeneId" = "100302278",
"source" = "mirbase",
"type" = "gene"
)
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = TRUE
)
expect_s4_class(object, "EnsemblTranscripts")
expect_length(object, n = 167L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSource" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000607096"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr1",
"start" = "30366",
"end" = "30503",
"width" = "138",
"strand" = "+",
"broadClass" = "small",
"ccdsId" = NA_character_,
"description" = paste(
"microRNA 1302-2",
"[Source:HGNC Symbol;Acc:HGNC:35294]"
),
"geneBiotype" = "miRNA",
"geneId" = "ENSG00000284332",
"geneIdVersion" = "ENSG00000284332.1",
"geneName" = "MIR1302-2",
"geneSource" = "mirbase",
"geneSynonyms" = "c(\"HSA-MIR-1302-2\", \"MIRN1302-2\")",
"ncbiGeneId" = "100302278",
"source" = "mirbase",
"tag" = "basic",
"txBiotype" = "miRNA",
"txId" = "ENST00000607096",
"txIdVersion" = "ENST00000607096.1",
"txName" = "MIR1302-2-201",
"txSource" = "mirbase",
"txSupportLevel" = NA_character_,
"type" = "transcript"
)
)
})
## See related issues:
## - https://github.com/Bioconductor/GenomeInfoDb/issues/97
## - https://github.com/Bioconductor/GenomeInfoDb/issues/98
test_that("getChromInfoFromEnsembl Seqinfo failure", {
file <- pasteUrl(
"ftp.ensembl.org",
"pub",
"release-90",
"gtf",
"mus_musculus",
"Mus_musculus.GRCm38.90.gtf.gz",
protocol = "ftp"
)
object <- makeGRangesFromGff(file, level = "genes")
expect_s4_class(object, "EnsemblGenes")
})
acidgenomics/AcidGenomes documentation built on Dec. 10, 2023, 10:35 p.m.
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test_that("Unsupported files", {
for (file in gffs[c(
"flybase_gff3",
"wormbase_gff3"
)]) {
expect_error(
object = makeGRangesFromGff(file = file),
regexp = "isSupportedGFF"
)
}
})
file <- gffs[["ensembl_grch38_gff3"]]
test_that("GFF3 genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = FALSE
)
expect_s4_class(object, "EnsemblGenes")
expect_length(object, 62703L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"logicName" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "CompressedCharacterList",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000116044.17"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "2",
"start" = "177218667",
"end" = "177392756",
"width" = "174090",
"strand" = "-",
"broadClass" = "coding",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"logicName" = "ensembl_havana_gene_homo_sapiens",
"ncbiGeneId" = "4780",
"source" = "ensembl_havana",
"tag" = "character(0)",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object))[seq_len(25L)],
expected = c(
"1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y", "MT"
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["1", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38.p13"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38.p13"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "0d9311600fa404a31f517b752002dcda"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
expect_identical(
object = metadata(object)[["release"]],
expected = 108L
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "4cf5bfc008e3a9b8d22d7613d989ee72dd7424dca552ce14cc3d5a87e0ca8048" # nolint
)
})
test_that("GFF3 transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "EnsemblTranscripts")
expect_length(object, 252300L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"logicName" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "CompressedCharacterList",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdNoVersion" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000397062.8"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "2",
"start" = "177230308",
"end" = "177264727",
"width" = "34420",
"strand" = "-",
"broadClass" = "coding",
"ccdsId" = "CCDS42782.1",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"logicName" = "ensembl_havana_gene_homo_sapiens",
"ncbiGeneId" = "4780",
"source" = "ensembl_havana",
"tag" = "c(\"basic\", \"Ensembl_canonical\", \"MANE_Select\")",
"txBiotype" = "protein_coding",
"txId" = "ENST00000397062.8",
"txIdNoVersion" = "ENST00000397062",
"txIdVersion" = "ENST00000397062.8",
"txName" = "NFE2L2-201",
"txSupportLevel" = "1 (assigned to previous version 7)",
"type" = "mRNA"
)
)
})
file <- gffs[["ensembl_grch38_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = FALSE
)
expect_s4_class(object, "EnsemblGenes")
expect_length(object, 62703L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000116044.17"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "2",
"start" = "177218667",
"end" = "177392756",
"width" = "174090",
"strand" = "-",
"broadClass" = "coding",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSource" = "ensembl_havana",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"ncbiGeneId" = "4780",
"source" = "ensembl_havana",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object))[seq_len(25L)],
expected = c(
"1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "X", "Y", "MT"
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["1", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38.p13"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38.p13"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "27864327a647f9fdae2cafff5f3ea45e"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
expect_identical(
object = metadata(object)[["release"]],
expected = 108L
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "1ae26267acf522d8d9a94736e2c00b5ff1008d43623fc73644092016ae0c57e8" # nolint
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "EnsemblTranscripts")
expect_length(object, 252301L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdNoVersion" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSource" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000397062.8"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "2",
"start" = "177230308",
"end" = "177264727",
"width" = "34420",
"strand" = "-",
"broadClass" = "coding",
"ccdsId" = "CCDS42782",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSource" = "ensembl_havana",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"ncbiGeneId" = "4780",
"source" = "ensembl_havana",
"tag" = "MANE_Select",
"txBiotype" = "protein_coding",
"txId" = "ENST00000397062.8",
"txIdNoVersion" = "ENST00000397062",
"txIdVersion" = "ENST00000397062.8",
"txName" = "NFE2L2-201",
"txSource" = "ensembl_havana",
"txSupportLevel" = "1 (assigned to previous version 7)",
"type" = "transcript"
)
)
})
file <- gffs[["flybase_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes"
)
expect_s4_class(object, "FlybaseGenes")
expect_length(object, 17896L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["FBgn0262975"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "3R",
"start" = "23185580",
"end" = "23226711",
"width" = "41132",
"strand" = "-",
"broadClass" = "other",
"geneId" = "FBgn0262975",
"geneName" = "cnc",
"source" = "FlyBase",
"type" = "gene"
)
)
expect_true(isSubset(
x = c(
"2L", "2R", "3L", "3R", "4", "X", "Y",
"mitochondrion_genome", "rDNA"
),
y = levels(seqnames(object))
))
expect_true(all(is.na(seqlengths(object))))
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "r6.49"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "722ba353d2dd6d3036d747f1498a2e9f"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Drosophila melanogaster"
)
expect_identical(
object = metadata(object)[["release"]],
expected = "r6.49"
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "565b486cbfe78942127482018e4439a28a6b171d71624d8ffe2a3611e162a101" # nolint
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts"
)
expect_s4_class(object, "FlybaseTranscripts")
expect_length(object, 35723L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"source" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["FBtr0306744"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "3R",
"start" = "23185580",
"end" = "23191120",
"width" = "5541",
"strand" = "-",
"broadClass" = "other",
"geneId" = "FBgn0262975",
"geneName" = "cnc",
"source" = "FlyBase",
"txId" = "FBtr0306744",
"txName" = "cnc-RF",
"type" = "mRNA"
)
)
})
file <- gffs[["gencode_grch38_gff3"]]
test_that("GFF3 genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = FALSE
)
expect_s4_class(object, "GencodeGenes")
expect_length(object, 62696L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"artifDupl" = "Rle",
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"havanaGene" = "Rle",
"hgncId" = "Rle",
"level" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "CompressedCharacterList",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000116044.17"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr2",
"start" = "177218667",
"end" = "177392756",
"width" = "174090",
"strand" = "-",
"artifDupl" = NA_character_,
"broadClass" = "coding",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"havanaGene" = "OTTHUMG00000133620.18",
"hgncId" = "HGNC:7782",
"level" = "1",
"ncbiGeneId" = "4780",
"source" = "HAVANA",
"tag" = "c(\"ncRNA_host\", \"overlapping_locus\")",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object)),
expected = paste0(
"chr",
c(
seq(from = 1L, to = 22L),
"X", "Y", "M"
)
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["chr1", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "b0199f8b1522f61093896e8d48750a0c"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
expect_identical(
object = metadata(object)[["release"]],
expected = 42L
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "10d01b26b75d0142677d0bddf369af375c2e24f6b4c99ce04f408032c51ca432" # nolint
)
})
test_that("GFF3 transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "GencodeTranscripts")
expect_length(object, 252416L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"havanaGene" = "Rle",
"havanaTranscript" = "Rle",
"hgncId" = "Rle",
"level" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"proteinId" = "Rle",
"source" = "Rle",
"tag" = "CompressedCharacterList",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdNoVersion" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000397062.8"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr2",
"start" = "177230308",
"end" = "177264727",
"width" = "34420",
"strand" = "-",
"broadClass" = "coding",
"ccdsId" = "CCDS42782.1",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"havanaGene" = "OTTHUMG00000133620.18",
"havanaTranscript" = "OTTHUMT00000257752.5",
"hgncId" = "HGNC:7782",
"level" = "2",
"ncbiGeneId" = "4780",
"proteinId" = "ENSP00000380252.3",
"source" = "HAVANA",
"tag" = paste(
"c(\"basic\",",
"\"Ensembl_canonical\",",
"\"MANE_Select\",",
"\"appris_alternative_1\",",
"\"CCDS\")"
),
"txBiotype" = "protein_coding",
"txId" = "ENST00000397062.8",
"txIdNoVersion" = "ENST00000397062",
"txIdVersion" = "ENST00000397062.8",
"txName" = "NFE2L2-201",
"txSupportLevel" = "1",
"type" = "transcript"
)
)
})
file <- gffs[["gencode_grch38_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = FALSE
)
expect_s4_class(object, "GencodeGenes")
expect_length(object, 62696L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"artifDupl" = "Rle",
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"havanaGene" = "Rle",
"hgncId" = "Rle",
"level" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000116044.17"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr2",
"start" = "177218667",
"end" = "177392756",
"width" = "174090",
"strand" = "-",
"artifDupl" = NA_character_,
"broadClass" = "coding",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"havanaGene" = "OTTHUMG00000133620.18",
"hgncId" = "HGNC:7782",
"level" = "1",
"ncbiGeneId" = "4780",
"source" = "HAVANA",
"tag" = "overlapping_locus",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object)),
expected = paste0(
"chr",
c(
seq(from = 1L, to = 22L),
"X", "Y", "M"
)
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["chr1", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "b3a1bb9b1239d8075dd2b031817a36da"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
expect_identical(
object = metadata(object)[["release"]],
expected = 42L
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "f59a5b38c6de1472430ccd0181927a01df0b4ad8d78f598e521badc9da80a76e" # nolint
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "GencodeTranscripts")
expect_length(object, 252416L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdNoVersion" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"havanaGene" = "Rle",
"havanaTranscript" = "Rle",
"hgncId" = "Rle",
"level" = "Rle",
"ncbiGeneId" = "CompressedIntegerList",
"proteinId" = "Rle",
"source" = "Rle",
"tag" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdNoVersion" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000397062.8"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr2",
"start" = "177230308",
"end" = "177264727",
"width" = "34420",
"strand" = "-",
"broadClass" = "coding",
"ccdsId" = "CCDS42782.1",
"description" = paste(
"NFE2 like bZIP transcription factor 2",
"[Source:HGNC Symbol;Acc:HGNC:7782]"
),
"geneBiotype" = "protein_coding",
"geneId" = "ENSG00000116044.17",
"geneIdNoVersion" = "ENSG00000116044",
"geneIdVersion" = "ENSG00000116044.17",
"geneName" = "NFE2L2",
"geneSynonyms" = "c(\"NRF-2\", \"NRF2\")",
"havanaGene" = "OTTHUMG00000133620.18",
"havanaTranscript" = "OTTHUMT00000257752.5",
"hgncId" = "HGNC:7782",
"level" = "2",
"ncbiGeneId" = "4780",
"proteinId" = "ENSP00000380252.3",
"source" = "HAVANA",
"tag" = "CCDS",
"txBiotype" = "protein_coding",
"txId" = "ENST00000397062.8",
"txIdNoVersion" = "ENST00000397062",
"txIdVersion" = "ENST00000397062.8",
"txName" = "NFE2L2-201",
"txSupportLevel" = "1",
"type" = "transcript"
)
)
})
file <- gffs[["refseq_grch38_gff3"]]
test_that("GFF3 genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes"
)
expect_s4_class(object, "RefseqGenes")
expect_identical(
object = lapply(mcols(object[[1L]]), simpleClass),
expected = list(
"broadClass" = "Rle",
"dbxref" = "CompressedCharacterList",
"description" = "Rle",
"exception" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSynonym" = "CompressedCharacterList",
"ncbiGeneId" = "Rle",
"parentGeneId" = "Rle",
"partial" = "Rle",
"pseudo" = "Rle",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = lapply(
X = as.data.frame(object[["AATF"]]),
FUN = as.character
),
expected = list(
"seqnames" = c("NC_000017.11", "NT_187614.1"),
"start" = c("36948954", "1185319"),
"end" = c("37056871", "1293236"),
"width" = rep("107918", 2L),
"strand" = rep("+", 2L),
"broadClass" = rep("coding", 2L),
"dbxref" = c(
"c(\"GeneID:26574\", \"HGNC:HGNC:19235\", \"MIM:608463\")",
"c(\"GeneID:26574\", \"HGNC:HGNC:19235\", \"MIM:608463\")"
),
"description" =
rep("apoptosis antagonizing transcription factor", 2L),
"exception" = rep(NA_character_, 2L),
"geneBiotype" = rep("protein_coding", 2L),
"geneId" = rep("AATF", 2L),
"geneName" = rep("AATF", 2L),
"geneSynonym" =
rep("c(\"BFR2\", \"CHE-1\", \"CHE1\", \"DED\")", 2L),
"ncbiGeneId" = rep("26574", 2L),
"parentGeneId" = c("AATF", "AATF-2"),
"partial" = rep(NA_character_, 2L),
"pseudo" = rep(NA_character_, 2L),
"source" = c("BestRefSeq%2CGnomon", "BestRefSeq%2CGnomon"),
"type" = rep("gene", 2L)
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["NC_000001.11", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38.p14"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38.p14"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
})
test_that("GFF3 transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts"
)
expect_s4_class(object, "RefseqTranscripts")
expect_true(all(grepl(
pattern = "^[A-Z]{2}_[0-9]+\\.[0-9]+$",
x = names(object)
)))
expect_identical(
object = lapply(mcols(object[[1L]]), simpleClass),
expected = list(
"broadClass" = "Rle",
"dbxref" = "CompressedCharacterList",
"description" = "Rle",
"exception" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSynonym" = "CompressedCharacterList",
"inference" = "Rle",
"modelEvidence" = "Rle",
"ncbiGeneId" = "Rle",
"parentGeneId" = "Rle",
"partial" = "Rle",
"product" = "Rle",
"pseudo" = "Rle",
"source" = "Rle",
"tag" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object[["NM_000014.6"]]),
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "NC_000012.12",
"start" = "9067708",
"end" = "9115919",
"width" = "48212",
"strand" = "-",
"broadClass" = "coding",
"dbxref" = paste(
"c(\"Ensembl:ENST00000318602.12\",",
"\"GeneID:2\",",
"\"GenBank:NM_000014.6\",",
"\"HGNC:HGNC:7\",",
"\"MIM:103950\")"
),
"description" = "alpha-2-macroglobulin",
"exception" = NA_character_,
"geneBiotype" = "protein_coding",
"geneId" = "A2M",
"geneName" = "A2M",
"geneSynonym" = "character(0)",
"inference" = NA_character_,
"modelEvidence" = NA_character_,
"ncbiGeneId" = "2",
"parentGeneId" = "A2M",
"partial" = NA_character_,
"product" = "alpha-2-macroglobulin, transcript variant 1",
"pseudo" = NA_character_,
"source" = "BestRefSeq",
"tag" = "MANE Select",
"txId" = "NM_000014.6",
"txName" = "NM_000014.6",
"type" = "mRNA"
)
)
})
file <- gffs[["refseq_grch38_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes"
)
expect_s4_class(object, "RefseqGenes")
expect_identical(
object = lapply(mcols(object[[1L]]), simpleClass),
expected = list(
"broadClass" = "Rle",
"dbXref" = "Rle",
"description" = "Rle",
"exception" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSynonym" = "Rle",
"ncbiGeneId" = "Rle",
"parentGeneId" = "Rle",
"partial" = "Rle",
"pseudo" = "Rle",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = lapply(
X = as.data.frame(object[["AATF"]]),
FUN = as.character
),
expected = list(
"seqnames" = c("NC_000017.11", "NT_187614.1"),
"start" = c("36948954", "1185319"),
"end" = c("37056871", "1293236"),
"width" = rep("107918", 2L),
"strand" = rep("+", 2L),
"broadClass" = rep("coding", 2L),
"dbXref" = rep("MIM:608463", 2L),
"description" =
rep("apoptosis antagonizing transcription factor", 2L),
"exception" = rep(NA_character_, 2L),
"geneBiotype" = rep("protein_coding", 2L),
"geneId" = rep("AATF", 2L),
"geneName" = rep("AATF", 2L),
"geneSynonym" = rep("DED", 2L),
"ncbiGeneId" = rep("26574", 2L),
"parentGeneId" = c("AATF", "AATF_1"),
"partial" = rep(NA_character_, 2L),
"pseudo" = rep(NA_character_, 2L),
"source" = c("BestRefSeq%2CGnomon", "BestRefSeq%2CGnomon"),
"type" = rep("gene", 2L)
)
)
expect_identical(
object = as.data.frame(seqinfo(object))["NC_000001.11", , drop = TRUE],
expected = list(
"seqlengths" = 248956422L,
"isCircular" = NA,
"genome" = "GRCh38.p14"
)
)
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "GRCh38.p14"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts"
)
expect_s4_class(object, "RefseqTranscripts")
expect_true(all(grepl(
pattern = "^[A-Z]{2}_[0-9]+\\.[0-9]+$",
x = names(object)
)))
expect_identical(
object = lapply(mcols(object[[1L]]), simpleClass),
expected = list(
"broadClass" = "Rle",
"dbXref" = "Rle",
"description" = "Rle",
"exception" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"inference" = "Rle",
"modelEvidence" = "Rle",
"ncbiGeneId" = "Rle",
"parentGeneId" = "Rle",
"partial" = "Rle",
"product" = "Rle",
"pseudo" = "Rle",
"source" = "Rle",
"tag" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object[["NM_000014.6"]]),
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "NC_000012.12",
"start" = "9067708",
"end" = "9115919",
"width" = "48212",
"strand" = "-",
"broadClass" = "coding",
"dbXref" = "GeneID:2",
"description" = "alpha-2-macroglobulin",
"exception" = NA_character_,
"geneBiotype" = "protein_coding",
"geneId" = "A2M",
"geneName" = "A2M",
"inference" = NA_character_,
"modelEvidence" = NA_character_,
"ncbiGeneId" = "2",
"parentGeneId" = "A2M",
"partial" = NA_character_,
"product" = "alpha-2-macroglobulin, transcript variant 1",
"pseudo" = NA_character_,
"source" = "BestRefSeq",
"tag" = "MANE Select",
"txBiotype" = "mRNA",
"txId" = "NM_000014.6",
"txName" = "NM_000014.6",
"type" = "transcript"
)
)
})
file <- gffs[["ucsc_hg38_ncbirefseq_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = TRUE
)
expect_s4_class(object, "UcscGenes")
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"geneId" = "Rle",
"geneName" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["A1BG"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr19",
"start" = "58345183",
"end" = "58353492",
"width" = "8310",
"strand" = "-",
"geneId" = "A1BG",
"geneName" = "A1BG"
)
)
## UCSC has changed some things related to hg38 that is currently causing
## issues with GenomeInfoDb (v1.34.7).
## https://github.com/Bioconductor/GenomeInfoDb/issues/83
## > expect_identical(
## > object = as.data.frame(seqinfo(object))["chr1", , drop = TRUE],
## > expected = list(
## > "seqlengths" = 248956422L,
## > "isCircular" = FALSE,
## > "genome" = "hg38"
## > )
## > )
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "hg38"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = FALSE
)
expect_s4_class(object, "UcscTranscripts")
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"geneId" = "Rle",
"geneName" = "Rle",
"txBiotype" = "Rle",
"txChrom" = "Rle",
"txEnd" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"txNumber" = "Rle",
"txStart" = "Rle",
"txStrand" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ABCA3P1_2"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr16",
"start" = "21938865",
"end" = "21940466",
"width" = "1602",
"strand" = "+",
"geneId" = "ABCA3P1",
"geneName" = "ABCA3P1",
"txBiotype" = "transcript",
"txChrom" = "chr16",
"txEnd" = "21940466",
"txId" = "ABCA3P1_2",
"txName" = "ABCA3P1_2",
"txNumber" = "144018",
"txStart" = "21938865",
"txStrand" = "+"
)
)
})
file <- gffs[["wormbase_gtf"]]
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes"
)
expect_s4_class(object, "WormbaseGenes")
expect_length(object, 46928L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneVersion" = "Rle",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["WBGene00022276"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "I",
"start" = "11495",
"end" = "16837",
"width" = "5343",
"strand" = "+",
"broadClass" = "coding",
"geneBiotype" = "protein_coding",
"geneId" = "WBGene00022276",
"geneName" = "nlp-40",
"geneSource" = "WormBase",
"geneVersion" = "1",
"source" = "WormBase",
"type" = "gene"
)
)
expect_identical(
object = levels(seqnames(object)),
expected = c(
"I",
"II",
"III",
"IV",
"V",
"X",
"MtDNA"
)
)
expect_true(all(is.na(seqlengths(object))))
expect_identical(
object = metadata(object)[["url"]],
expected = file
)
expect_true(
isAFile(metadata(object)[["file"]])
)
expect_identical(
object = metadata(object)[["genomeBuild"]],
expected = "WS287"
)
expect_identical(
object = metadata(object)[["md5"]],
expected = "5c45625e18ee2b5d4b9830da34cd01bf"
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Caenorhabditis elegans"
)
expect_identical(
object = metadata(object)[["release"]],
expected = "WS287"
)
expect_identical(
object = metadata(object)[["sha256"]],
expected = "6b8756bd1dfd5995e0c242d35bf3b3d3b04208a65cbf16bc7bfb9befb9a3684f" # nolint
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts"
)
expect_s4_class(object, "WormbaseTranscripts")
expect_length(object, 60136L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneVersion" = "Rle",
"source" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txName" = "Rle",
"txSource" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["Y74C9A.2a.3"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "I",
"start" = "11495",
"end" = "16793",
"width" = "5299",
"strand" = "+",
"broadClass" = "coding",
"geneBiotype" = "protein_coding",
"geneId" = "WBGene00022276",
"geneName" = "nlp-40",
"geneSource" = "WormBase",
"geneVersion" = "1",
"source" = "WormBase",
"txBiotype" = "protein_coding",
"txId" = "Y74C9A.2a.3",
"txName" = "Y74C9A.2a.3",
"txSource" = "WormBase",
"type" = "transcript"
)
)
})
file <- file.path(cacheDir, "ref-transcripts.gtf")
test_that("GTF genes", {
object <- makeGRangesFromGff(
file = file,
level = "genes",
ignoreVersion = TRUE
)
expect_s4_class(object, "EnsemblGenes")
expect_length(object, n = 60L)
expect_named(
object = object,
expected = as.character(mcols(object)[["geneId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENSG00000284332"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr1",
"start" = "30366",
"end" = "30503",
"width" = "138",
"strand" = "+",
"broadClass" = "small",
"description" = paste(
"microRNA 1302-2",
"[Source:HGNC Symbol;Acc:HGNC:35294]"
),
"geneBiotype" = "miRNA",
"geneId" = "ENSG00000284332",
"geneIdVersion" = "ENSG00000284332.1",
"geneName" = "MIR1302-2",
"geneSource" = "mirbase",
"geneSynonyms" = "c(\"HSA-MIR-1302-2\", \"MIRN1302-2\")",
"ncbiGeneId" = "100302278",
"source" = "mirbase",
"type" = "gene"
)
)
expect_identical(
object = metadata(object)[["organism"]],
expected = "Homo sapiens"
)
})
test_that("GTF transcripts", {
object <- makeGRangesFromGff(
file = file,
level = "transcripts",
ignoreVersion = TRUE
)
expect_s4_class(object, "EnsemblTranscripts")
expect_length(object, n = 167L)
expect_named(
object = object,
expected = as.character(mcols(object)[["txId"]])
)
expect_identical(
object = lapply(mcols(object), simpleClass),
expected = list(
"broadClass" = "Rle",
"ccdsId" = "Rle",
"description" = "Rle",
"geneBiotype" = "Rle",
"geneId" = "Rle",
"geneIdVersion" = "Rle",
"geneName" = "Rle",
"geneSource" = "Rle",
"geneSynonyms" = "CompressedCharacterList",
"ncbiGeneId" = "CompressedIntegerList",
"source" = "Rle",
"tag" = "Rle",
"txBiotype" = "Rle",
"txId" = "Rle",
"txIdVersion" = "Rle",
"txName" = "Rle",
"txSource" = "Rle",
"txSupportLevel" = "Rle",
"type" = "Rle"
)
)
expect_identical(
object = vapply(
X = as.data.frame(object["ENST00000607096"]), # nolint
FUN = as.character,
FUN.VALUE = character(1L)
),
expected = c(
"seqnames" = "chr1",
"start" = "30366",
"end" = "30503",
"width" = "138",
"strand" = "+",
"broadClass" = "small",
"ccdsId" = NA_character_,
"description" = paste(
"microRNA 1302-2",
"[Source:HGNC Symbol;Acc:HGNC:35294]"
),
"geneBiotype" = "miRNA",
"geneId" = "ENSG00000284332",
"geneIdVersion" = "ENSG00000284332.1",
"geneName" = "MIR1302-2",
"geneSource" = "mirbase",
"geneSynonyms" = "c(\"HSA-MIR-1302-2\", \"MIRN1302-2\")",
"ncbiGeneId" = "100302278",
"source" = "mirbase",
"tag" = "basic",
"txBiotype" = "miRNA",
"txId" = "ENST00000607096",
"txIdVersion" = "ENST00000607096.1",
"txName" = "MIR1302-2-201",
"txSource" = "mirbase",
"txSupportLevel" = NA_character_,
"type" = "transcript"
)
)
})
## See related issues:
## - https://github.com/Bioconductor/GenomeInfoDb/issues/97
## - https://github.com/Bioconductor/GenomeInfoDb/issues/98
test_that("getChromInfoFromEnsembl Seqinfo failure", {
file <- pasteUrl(
"ftp.ensembl.org",
"pub",
"release-90",
"gtf",
"mus_musculus",
"Mus_musculus.GRCm38.90.gtf.gz",
protocol = "ftp"
)
object <- makeGRangesFromGff(file, level = "genes")
expect_s4_class(object, "EnsemblGenes")
})
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