tests/testthat/test_transcriptToX.R
In jorainer/ensembldb: Utilities to create and use Ensembl-based annotation databases
test_that(".tx_to_protein works", {
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name %in% c("X", "Y"))
## SHOX2, ENST00000381578
## exon 1: 259
## exon 2: 709 UTR: 432nt long
## exon 3: 209
## exon 4: 58
## exon 5: 89
## exon 6: 2,433 CDS: 246, then UTR.
x <- IRanges(start = 2, width = 4)
expect_error(.tx_to_protein(x, edbx))
expect_error(.txs_to_proteins(x, edbx))
## Non existant transcript.
x <- IRanges(start = 2, width = 5, names = "some")
expect_warning(res_a <- .tx_to_protein(x, edbx))
expect_true(is(res_a, "IRanges"))
expect_equal(colnames(mcols(res_a)), c("tx_id", "tx_start", "tx_end",
"cds_ok"))
expect_true(start(res_a) < 0)
expect_warning(res_b <- .txs_to_proteins(x, edbx))
expect_equal(res_a, res_b)
## ENST00000431238: non-coding transcript
x <- IRanges(start = 2, width = 5, names = "ENST00000431238")
expect_warning(res_a <- .tx_to_protein(x, edbx))
expect_true(is(res_a, "IRanges"))
expect_equal(colnames(mcols(res_a)), c("tx_id", "tx_start", "tx_end",
"cds_ok"))
expect_true(start(res_a) < 0)
expect_warning(res_b <- .txs_to_proteins(x, edbx))
expect_equal(res_a, res_b)
## just outside the CDS
x <- IRanges(start = 691, width = 1, names = "ENST00000381578")
expect_warning(res_a <- .tx_to_protein(x, edbx))
expect_true(is(res_a, "IRanges"))
expect_equal(colnames(mcols(res_a)), c("tx_id", "tx_start", "tx_end",
"cds_ok"))
expect_true(start(res_a) < 0)
expect_warning(res_b <- .txs_to_proteins(x, edbx))
expect_equal(res_a, res_b)
## first 2nt of the CDS
x <- IRanges(start = 692, width = 2, names = "ENST00000381578")
res_a <- .tx_to_protein(x, edbx)
expect_equal(start(res_a), 1)
expect_equal(end(res_a), 1)
expect_true(mcols(res_a)$cds_ok)
res_b <- .txs_to_proteins(x, edbx)
expect_equal(res_a, res_b)
## nt 3-4 of the CDS, should map to 1-2 of the prot seq.
x <- IRanges(start = 694, width = 2, names = "ENST00000381578")
res_a <- .tx_to_protein(x, edbx)
expect_equal(start(res_a), 1)
expect_equal(end(res_a), 2)
## nts of the stop codon.
x <- IRanges(start = 1569, width = 4, names = "ENST00000381578")
expect_warning(res_a <- .tx_to_protein(x, edbx))
## last nt before the stop codon
x <- IRanges(start = 1567, width = 1, names = "ENST00000381578")
res_a <- .tx_to_protein(x, edbx)
prt <- proteins(edbx, filter = ProteinIdFilter(names(res_a)))
expect_equal(start(res_a), nchar(prt$protein_sequence))
x <- IRanges(start = 692, width = 2)
mcols(x)$id <- "ENST00000381578"
res_a <- .tx_to_protein(x, edbx, id = "id")
res_b <- .txs_to_proteins(x, edbx, id = "id")
mcols(res_b) <- mcols(res_b)[1:4]
expect_equal(res_a, res_b)
## Multiple input.
## just outside the CDS (last nt of the 5' UTR).
x <- IRanges(start = c(691, 692, 32, 5000, 1, 1565),
width = c(1, 1, 3, 3, 2, 2),
names = c("ENST00000381578", "ENST00000381578", "some",
"ENST00000381578", "ENST00000431238",
"ENST00000381578"))
expect_warning(res_a <- .tx_to_protein(x, edbx))
expect_warning(res_b <- .txs_to_proteins(x, edbx))
expect_equal(res_a, res_b)
## Preloaded data test
proteins <- proteins(edbx)
exons <- exonsBy(edbx)
transcripts <- transcripts(edbx)
expect_warning(res_c <- .txs_to_proteins(x, edbx,
proteins = proteins,
exons = exons,
transcripts = transcripts))
expect_equal(res_c, res_b)
})
test_that("transcriptToProtein works", {
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "X")
## Errors.
expect_error(transcriptToProtein())
expect_error(transcriptToProtein(db = edbx))
expect_error(transcriptToProtein(txpos))
##
x <- IRanges(start = 692, width = 2)
mcols(x)$id <- "ENST00000381578"
expect_error(transcriptToProtein(x))
res <- transcriptToProtein(x, edbx, id = "id")
expect_equal(start(res), 1)
expect_equal(end(res), 1)
## Preloaded data test
proteins <- proteins(edbx)
exons <- exonsBy(edbx)
transcripts <- transcripts(edbx)
expect_error(transcriptToProtein(x, edbx, id = "id",
exons = exons,
transcripts = transcripts))
expect_error(transcriptToProtein(x, edbx,
proteins = proteins,
exons = exons,
transcripts = transcripts))
expect_error(transcriptToProtein(x, edbx, id = "id",
proteins = proteins,
exons = proteins,
transcripts = transcripts))
res2 <- transcriptToProtein(x, edbx, id = "id", proteins = proteins, exons = exons, transcripts = transcripts)
expect_equal(res2, res)
})
test_that(".tx_to_genome works", {
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name %in% c("X", "Y"))
## ENST00000486554:501:505 106959129:106959131 106957979:106957979 -
## ENST00000486554:1:5 106959627:106959631 -
## ENST00000381578:1:5 585079:585083 +
## ENST00000381578:259:260 585337:585337 591201:591201 +
## some:1:4 NA
## ENST00000155093:2:3 2935478:29935479 +
rng <- IRanges(start = c(501, 1, 1, 259, 1, 2),
end = c(505, 5, 5, 260, 4, 3),
names = c("ENST00000486554", "ENST00000486554",
"ENST00000381578", "ENST00000381578", "some",
"ENST00000155093"))
res <- ensembldb:::.tx_to_genome(rng, edbx)
expect_equal(length(res), length(rng))
expect_equal(unname(lengths(res)), c(2, 1, 1, 2, 0, 1))
## 1
expect_equal(start(res[[1]]), c(107715899, 107714749))
expect_equal(end(res[[1]]), c(107715901, 107714749))
expect_equal(as.character(strand(res[[1]])), c("-", "-"))
## 2
expect_equal(start(res[[2]]), 107716397)
expect_equal(end(res[[2]]), 107716401)
expect_equal(as.character(strand(res[[2]])), "-")
## 3
expect_equal(start(res[[3]]), 624344)
expect_equal(end(res[[3]]), 624348)
expect_equal(as.character(strand(res[[3]])), "+")
## 4
expect_equal(start(res[[4]]), c(624602, 630466))
expect_equal(end(res[[4]]), c(624602, 630466))
expect_equal(as.character(strand(res[[4]])), c("+", "+"))
## 6
expect_equal(start(res[[6]]), 2935478)
expect_equal(end(res[[6]]), 2935479)
expect_equal(as.character(strand(res[[6]])), "+")
expect_equal(as.character(seqnames(res[[6]])), "Y")
## add pre-load data test
exons <- exonsBy(edbx)
res_preload <- unlist(ensembldb:::.tx_to_genome(rng, exons))
res_unlisted <- unlist(res)
res_unlisted$tx_id <- NULL
seqlevels(res_preload) <- seqlevels(res_unlisted)
expect_equal(res_unlisted, res_preload)
## wrong ID and range outside tx
rng <- IRanges(start = c(501, 200, 1), end = c(505, 1200, 5),
names = c("ENST00000486554", "ENST00000486554", "B"))
expect_warning(res_2 <- ensembldb:::.tx_to_genome(rng, edbx))
a <- unlist(res[1])
b <- unlist(res_2[1])
seqlevels(a) <- seqlevels(b)
expect_equal(a, b)
expect_equal(lengths(res_2), c(ENST00000486554 = 2, ENST00000486554 = 0,
B = 0))
## add pre-load data test
expect_warning(res_3 <- ensembldb:::.tx_to_genome(rng, exons))
c <- unlist(res_3[1])
seqlevels(res_preload) <- seqlevels(c)
expect_equal(res_preload, res_preload)
expect_equal(lengths(res_3), c(ENST00000486554 = 2, ENST00000486554 = 0,
B = 0))
})
test_that("transcriptToGenome works", {
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "X")
x <- IRanges(start = c(259, 1, 259), end = c(260, 4, 261),
names = c("ENST00000381578", "some", "ENST00000381578"))
## Errors.
expect_error(transcriptToGenome())
expect_error(transcriptToGenome(db = edbx))
expect_error(transcriptToGenome(x))
expect_warning(res <- transcriptToGenome(x, edbx))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == length(x))
expect_true(length(res[[2]]) == 0)
expect_equal(names(res), names(x))
expect_equal(start(res[[1]]), start(res[[3]]))
expect_equal(end(res[[1]])[1], end(res[[3]])[1])
expect_equal(end(res[[1]])[2] + 1, end(res[[3]])[2])
expect_warning(res <- transcriptToGenome(x[2], edbx))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 1)
expect_warning(res <- transcriptToGenome(x[c(2, 2)], edbx))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 2)
res <- transcriptToGenome(x[1], edbx)
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 1)
expect_true(length(res[[1]]) == 2)
x <- IRanges(start = c(256, 2), end = c(265, 12000),
names = c("ENST00000381578", "ENST00000381578"))
expect_warning(res <- transcriptToGenome(x, edbx)) # indeed warn expected
expect_equal(lengths(res), c(ENST00000381578 = 2, ENST00000381578 = 0))
## add pre-load data test
exons <- exonsBy(edbx)
x <- IRanges(start = c(259, 1, 259), end = c(260, 4, 261),
names = c("ENST00000381578", "some", "ENST00000381578"))
expect_warning(res <- transcriptToGenome(x, exons))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == length(x))
expect_true(length(res[[2]]) == 0)
expect_equal(names(res), names(x))
expect_equal(start(res[[1]]), start(res[[3]]))
expect_equal(end(res[[1]])[1], end(res[[3]])[1])
expect_equal(end(res[[1]])[2] + 1, end(res[[3]])[2])
expect_warning(res <- transcriptToGenome(x[2], exons))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 1)
expect_warning(res <- transcriptToGenome(x[c(2, 2)], exons))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 2)
res <- transcriptToGenome(x[1], exons)
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 1)
expect_true(length(res[[1]]) == 2)
x <- IRanges(start = c(256, 2), end = c(265, 12000),
names = c("ENST00000381578", "ENST00000381578"),
info = 'ORFs')
expect_warning(res <- transcriptToGenome(x, exons))
expect_true(res$ENST00000381578$info[1] == 'ORFs')
expect_equal(lengths(res), c(ENST00000381578 = 2, ENST00000381578 = 0))
})
test_that("transcriptToCds works", {
expect_error(transcriptToCds())
edb18 <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "18")
expect_error(transcriptToCds(db = edb18))
## 1) unknown tx ids
txcoords <- IRanges(start = c(4, 3), width = c(1, 1), names = c("a", "b"))
expect_error(transcriptToCds(x = txcoords))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_true(all(start(res) == -1))
expect_true(all(end(res) == -1))
## 2) all tx not coding
txcoords <- IRanges(start = c(132, 133), end = c(323, 323),
names = rep("ENST00000590515", 2))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_true(all(start(res) == -1))
expect_true(all(end(res) == -1))
## 3) some tx not coding
## 4) coordinate not within coding
txcoords <- IRanges(start = c(1463, 3, 143, 147, 1463), width = 1,
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955",
"ENST00000398117"))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_equal(start(res), c(1, -1, -1, 1, 1))
expect_equal(end(res), c(1, -1, -1, 1, 1))
expect_equal(res[1], res[5])
## End position outside of CDS
txcoords <- IRanges(start = c(1463, 3, 143, 147), width = c(4, 1, 1, 765),
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_equal(start(res), c(1, -1, -1, -1))
expect_equal(end(res), c(4, -1, -1, -1))
txcoords <- IRanges(start = c(3, 143, 147), width = c(1, 1, 765),
names = c("ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_true(all(start(res) < 0))
expect_true(all(end(res) < 0))
## Preloaded data test
exons <- exonsBy(edb18)
transcripts <- transcripts(edb18)
expect_error(transcriptToCds(db = edb18, exons = exons,transcripts = transcripts))
## 1) unknown tx ids
txcoords <- IRanges(start = c(4, 3), width = c(1, 1), names = c("a", "b"))
expect_error(transcriptToCds(x = txcoords))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_true(all(start(res) == -1))
expect_true(all(end(res) == -1))
## 2) all tx not coding
txcoords <- IRanges(start = c(132, 133), end = c(323, 323),
names = rep("ENST00000590515", 2))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_true(all(start(res) == -1))
expect_true(all(end(res) == -1))
## 3) some tx not coding
## 4) coordinate not within coding
txcoords <- IRanges(start = c(1463, 3, 143, 147, 1463), width = 1,
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955",
"ENST00000398117"))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_equal(start(res), c(1, -1, -1, 1, 1))
expect_equal(end(res), c(1, -1, -1, 1, 1))
expect_equal(res[1], res[5])
## End position outside of CDS
txcoords <- IRanges(start = c(1463, 3, 143, 147), width = c(4, 1, 1, 765),
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_equal(start(res), c(1, -1, -1, -1))
expect_equal(end(res), c(4, -1, -1, -1))
txcoords <- IRanges(start = c(3, 143, 147), width = c(1, 1, 765),
names = c("ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_true(all(start(res) < 0))
expect_true(all(end(res) < 0))
})
test_that("cdsToTranscript works", {
edb18 <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "18")
expect_error(cdsToTranscript())
expect_error(cdsToTranscript(db = edb18))
txcoords <- IRanges(start = c(4, 3, 143, 147), width = 1,
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_error(cdsToTranscript(x = txcoords))
expect_warning(res <- cdsToTranscript(txcoords, edb18))
expect_equal(start(res), c(1466, 902, -1, 293))
txcoords <- IRanges(start = c(4, 3, 50000, 147), width = 1,
names = c("ENST00000398117", "ENST00000398117",
"ENST00000398117", "b"))
expect_warning(res <- cdsToTranscript(txcoords, edb18))
expect_equal(start(res), c(1466, 1465, -1, -1))
## Map variants:
## ENST00000070846:c.1643DelG
## ENST00000070846:c.1881DelC
## ENST00000379802:c.6995C>A
## ENST00000261590:c.1088C>T
## ENST00000261590:c.561T>G
rngs <- IRanges(start = c(1643, 1881, 6995, 1088, 561), width = 1,
names = c("ENST00000070846", "ENST00000070846",
"ENST00000379802", "ENST00000261590",
"ENST00000261590"))
rngs_tx <- cdsToTranscript(rngs, EnsDb.Hsapiens.v86)
gnm <- transcriptToGenome(rngs_tx, EnsDb.Hsapiens.v86)
library(BSgenome.Hsapiens.NCBI.GRCh38)
res <- getSeq(BSgenome.Hsapiens.NCBI.GRCh38, unlist(gnm))
exp <- c("G", "C", "C", "C", "T")
expect_equal(exp, unname(as.character(res)))
## Preloaded data test
exons <- exonsBy(EnsDb.Hsapiens.v86)
transcripts <- transcripts(EnsDb.Hsapiens.v86)
edb18 <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "18")
expect_error(cdsToTranscript())
expect_error(cdsToTranscript(db = edb18, exons = exons,transcripts = transcripts))
txcoords <- IRanges(start = c(4, 3, 143, 147), width = 1,
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_error(cdsToTranscript(x = txcoords))
expect_warning(res <- cdsToTranscript(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_equal(start(res), c(1466, 902, -1, 293))
txcoords <- IRanges(start = c(4, 3, 50000, 147), width = 1,
names = c("ENST00000398117", "ENST00000398117",
"ENST00000398117", "b"))
expect_warning(res <- cdsToTranscript(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_equal(start(res), c(1466, 1465, -1, -1))
## Map variants:
## ENST00000070846:c.1643DelG
## ENST00000070846:c.1881DelC
## ENST00000379802:c.6995C>A
## ENST00000261590:c.1088C>T
## ENST00000261590:c.561T>G
rngs <- IRanges(start = c(1643, 1881, 6995, 1088, 561), width = 1,
names = c("ENST00000070846", "ENST00000070846",
"ENST00000379802", "ENST00000261590",
"ENST00000261590"))
rngs_tx <- cdsToTranscript(rngs, EnsDb.Hsapiens.v86, exons = exons,transcripts = transcripts)
gnm <- transcriptToGenome(rngs_tx, exons)
library(BSgenome.Hsapiens.NCBI.GRCh38)
res <- getSeq(BSgenome.Hsapiens.NCBI.GRCh38, unlist(gnm))
exp <- c("G", "C", "C", "C", "T")
expect_equal(exp, unname(as.character(res)))
})
test_that(".ids_message works", {
res <- .ids_message(c("a", "b"))
expect_equal(res, paste(c("a", "b"), collapse = ", "))
res <- .ids_message(c("a", "b", "c", "d", "e", "f"))
expect_equal(res, "a, b, c ... (3 more)")
expect_equal(.ids_message(c("c", "b", "c", "d")), "c, b, c ... (1 more)")
})
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test_that(".tx_to_protein works", {
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name %in% c("X", "Y"))
## SHOX2, ENST00000381578
## exon 1: 259
## exon 2: 709 UTR: 432nt long
## exon 3: 209
## exon 4: 58
## exon 5: 89
## exon 6: 2,433 CDS: 246, then UTR.
x <- IRanges(start = 2, width = 4)
expect_error(.tx_to_protein(x, edbx))
expect_error(.txs_to_proteins(x, edbx))
## Non existant transcript.
x <- IRanges(start = 2, width = 5, names = "some")
expect_warning(res_a <- .tx_to_protein(x, edbx))
expect_true(is(res_a, "IRanges"))
expect_equal(colnames(mcols(res_a)), c("tx_id", "tx_start", "tx_end",
"cds_ok"))
expect_true(start(res_a) < 0)
expect_warning(res_b <- .txs_to_proteins(x, edbx))
expect_equal(res_a, res_b)
## ENST00000431238: non-coding transcript
x <- IRanges(start = 2, width = 5, names = "ENST00000431238")
expect_warning(res_a <- .tx_to_protein(x, edbx))
expect_true(is(res_a, "IRanges"))
expect_equal(colnames(mcols(res_a)), c("tx_id", "tx_start", "tx_end",
"cds_ok"))
expect_true(start(res_a) < 0)
expect_warning(res_b <- .txs_to_proteins(x, edbx))
expect_equal(res_a, res_b)
## just outside the CDS
x <- IRanges(start = 691, width = 1, names = "ENST00000381578")
expect_warning(res_a <- .tx_to_protein(x, edbx))
expect_true(is(res_a, "IRanges"))
expect_equal(colnames(mcols(res_a)), c("tx_id", "tx_start", "tx_end",
"cds_ok"))
expect_true(start(res_a) < 0)
expect_warning(res_b <- .txs_to_proteins(x, edbx))
expect_equal(res_a, res_b)
## first 2nt of the CDS
x <- IRanges(start = 692, width = 2, names = "ENST00000381578")
res_a <- .tx_to_protein(x, edbx)
expect_equal(start(res_a), 1)
expect_equal(end(res_a), 1)
expect_true(mcols(res_a)$cds_ok)
res_b <- .txs_to_proteins(x, edbx)
expect_equal(res_a, res_b)
## nt 3-4 of the CDS, should map to 1-2 of the prot seq.
x <- IRanges(start = 694, width = 2, names = "ENST00000381578")
res_a <- .tx_to_protein(x, edbx)
expect_equal(start(res_a), 1)
expect_equal(end(res_a), 2)
## nts of the stop codon.
x <- IRanges(start = 1569, width = 4, names = "ENST00000381578")
expect_warning(res_a <- .tx_to_protein(x, edbx))
## last nt before the stop codon
x <- IRanges(start = 1567, width = 1, names = "ENST00000381578")
res_a <- .tx_to_protein(x, edbx)
prt <- proteins(edbx, filter = ProteinIdFilter(names(res_a)))
expect_equal(start(res_a), nchar(prt$protein_sequence))
x <- IRanges(start = 692, width = 2)
mcols(x)$id <- "ENST00000381578"
res_a <- .tx_to_protein(x, edbx, id = "id")
res_b <- .txs_to_proteins(x, edbx, id = "id")
mcols(res_b) <- mcols(res_b)[1:4]
expect_equal(res_a, res_b)
## Multiple input.
## just outside the CDS (last nt of the 5' UTR).
x <- IRanges(start = c(691, 692, 32, 5000, 1, 1565),
width = c(1, 1, 3, 3, 2, 2),
names = c("ENST00000381578", "ENST00000381578", "some",
"ENST00000381578", "ENST00000431238",
"ENST00000381578"))
expect_warning(res_a <- .tx_to_protein(x, edbx))
expect_warning(res_b <- .txs_to_proteins(x, edbx))
expect_equal(res_a, res_b)
## Preloaded data test
proteins <- proteins(edbx)
exons <- exonsBy(edbx)
transcripts <- transcripts(edbx)
expect_warning(res_c <- .txs_to_proteins(x, edbx,
proteins = proteins,
exons = exons,
transcripts = transcripts))
expect_equal(res_c, res_b)
})
test_that("transcriptToProtein works", {
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "X")
## Errors.
expect_error(transcriptToProtein())
expect_error(transcriptToProtein(db = edbx))
expect_error(transcriptToProtein(txpos))
##
x <- IRanges(start = 692, width = 2)
mcols(x)$id <- "ENST00000381578"
expect_error(transcriptToProtein(x))
res <- transcriptToProtein(x, edbx, id = "id")
expect_equal(start(res), 1)
expect_equal(end(res), 1)
## Preloaded data test
proteins <- proteins(edbx)
exons <- exonsBy(edbx)
transcripts <- transcripts(edbx)
expect_error(transcriptToProtein(x, edbx, id = "id",
exons = exons,
transcripts = transcripts))
expect_error(transcriptToProtein(x, edbx,
proteins = proteins,
exons = exons,
transcripts = transcripts))
expect_error(transcriptToProtein(x, edbx, id = "id",
proteins = proteins,
exons = proteins,
transcripts = transcripts))
res2 <- transcriptToProtein(x, edbx, id = "id", proteins = proteins, exons = exons, transcripts = transcripts)
expect_equal(res2, res)
})
test_that(".tx_to_genome works", {
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name %in% c("X", "Y"))
## ENST00000486554:501:505 106959129:106959131 106957979:106957979 -
## ENST00000486554:1:5 106959627:106959631 -
## ENST00000381578:1:5 585079:585083 +
## ENST00000381578:259:260 585337:585337 591201:591201 +
## some:1:4 NA
## ENST00000155093:2:3 2935478:29935479 +
rng <- IRanges(start = c(501, 1, 1, 259, 1, 2),
end = c(505, 5, 5, 260, 4, 3),
names = c("ENST00000486554", "ENST00000486554",
"ENST00000381578", "ENST00000381578", "some",
"ENST00000155093"))
res <- ensembldb:::.tx_to_genome(rng, edbx)
expect_equal(length(res), length(rng))
expect_equal(unname(lengths(res)), c(2, 1, 1, 2, 0, 1))
## 1
expect_equal(start(res[[1]]), c(107715899, 107714749))
expect_equal(end(res[[1]]), c(107715901, 107714749))
expect_equal(as.character(strand(res[[1]])), c("-", "-"))
## 2
expect_equal(start(res[[2]]), 107716397)
expect_equal(end(res[[2]]), 107716401)
expect_equal(as.character(strand(res[[2]])), "-")
## 3
expect_equal(start(res[[3]]), 624344)
expect_equal(end(res[[3]]), 624348)
expect_equal(as.character(strand(res[[3]])), "+")
## 4
expect_equal(start(res[[4]]), c(624602, 630466))
expect_equal(end(res[[4]]), c(624602, 630466))
expect_equal(as.character(strand(res[[4]])), c("+", "+"))
## 6
expect_equal(start(res[[6]]), 2935478)
expect_equal(end(res[[6]]), 2935479)
expect_equal(as.character(strand(res[[6]])), "+")
expect_equal(as.character(seqnames(res[[6]])), "Y")
## add pre-load data test
exons <- exonsBy(edbx)
res_preload <- unlist(ensembldb:::.tx_to_genome(rng, exons))
res_unlisted <- unlist(res)
res_unlisted$tx_id <- NULL
seqlevels(res_preload) <- seqlevels(res_unlisted)
expect_equal(res_unlisted, res_preload)
## wrong ID and range outside tx
rng <- IRanges(start = c(501, 200, 1), end = c(505, 1200, 5),
names = c("ENST00000486554", "ENST00000486554", "B"))
expect_warning(res_2 <- ensembldb:::.tx_to_genome(rng, edbx))
a <- unlist(res[1])
b <- unlist(res_2[1])
seqlevels(a) <- seqlevels(b)
expect_equal(a, b)
expect_equal(lengths(res_2), c(ENST00000486554 = 2, ENST00000486554 = 0,
B = 0))
## add pre-load data test
expect_warning(res_3 <- ensembldb:::.tx_to_genome(rng, exons))
c <- unlist(res_3[1])
seqlevels(res_preload) <- seqlevels(c)
expect_equal(res_preload, res_preload)
expect_equal(lengths(res_3), c(ENST00000486554 = 2, ENST00000486554 = 0,
B = 0))
})
test_that("transcriptToGenome works", {
edbx <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "X")
x <- IRanges(start = c(259, 1, 259), end = c(260, 4, 261),
names = c("ENST00000381578", "some", "ENST00000381578"))
## Errors.
expect_error(transcriptToGenome())
expect_error(transcriptToGenome(db = edbx))
expect_error(transcriptToGenome(x))
expect_warning(res <- transcriptToGenome(x, edbx))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == length(x))
expect_true(length(res[[2]]) == 0)
expect_equal(names(res), names(x))
expect_equal(start(res[[1]]), start(res[[3]]))
expect_equal(end(res[[1]])[1], end(res[[3]])[1])
expect_equal(end(res[[1]])[2] + 1, end(res[[3]])[2])
expect_warning(res <- transcriptToGenome(x[2], edbx))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 1)
expect_warning(res <- transcriptToGenome(x[c(2, 2)], edbx))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 2)
res <- transcriptToGenome(x[1], edbx)
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 1)
expect_true(length(res[[1]]) == 2)
x <- IRanges(start = c(256, 2), end = c(265, 12000),
names = c("ENST00000381578", "ENST00000381578"))
expect_warning(res <- transcriptToGenome(x, edbx)) # indeed warn expected
expect_equal(lengths(res), c(ENST00000381578 = 2, ENST00000381578 = 0))
## add pre-load data test
exons <- exonsBy(edbx)
x <- IRanges(start = c(259, 1, 259), end = c(260, 4, 261),
names = c("ENST00000381578", "some", "ENST00000381578"))
expect_warning(res <- transcriptToGenome(x, exons))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == length(x))
expect_true(length(res[[2]]) == 0)
expect_equal(names(res), names(x))
expect_equal(start(res[[1]]), start(res[[3]]))
expect_equal(end(res[[1]])[1], end(res[[3]])[1])
expect_equal(end(res[[1]])[2] + 1, end(res[[3]])[2])
expect_warning(res <- transcriptToGenome(x[2], exons))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 1)
expect_warning(res <- transcriptToGenome(x[c(2, 2)], exons))
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 2)
res <- transcriptToGenome(x[1], exons)
expect_true(is(res, "GRangesList"))
expect_true(length(res) == 1)
expect_true(length(res[[1]]) == 2)
x <- IRanges(start = c(256, 2), end = c(265, 12000),
names = c("ENST00000381578", "ENST00000381578"),
info = 'ORFs')
expect_warning(res <- transcriptToGenome(x, exons))
expect_true(res$ENST00000381578$info[1] == 'ORFs')
expect_equal(lengths(res), c(ENST00000381578 = 2, ENST00000381578 = 0))
})
test_that("transcriptToCds works", {
expect_error(transcriptToCds())
edb18 <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "18")
expect_error(transcriptToCds(db = edb18))
## 1) unknown tx ids
txcoords <- IRanges(start = c(4, 3), width = c(1, 1), names = c("a", "b"))
expect_error(transcriptToCds(x = txcoords))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_true(all(start(res) == -1))
expect_true(all(end(res) == -1))
## 2) all tx not coding
txcoords <- IRanges(start = c(132, 133), end = c(323, 323),
names = rep("ENST00000590515", 2))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_true(all(start(res) == -1))
expect_true(all(end(res) == -1))
## 3) some tx not coding
## 4) coordinate not within coding
txcoords <- IRanges(start = c(1463, 3, 143, 147, 1463), width = 1,
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955",
"ENST00000398117"))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_equal(start(res), c(1, -1, -1, 1, 1))
expect_equal(end(res), c(1, -1, -1, 1, 1))
expect_equal(res[1], res[5])
## End position outside of CDS
txcoords <- IRanges(start = c(1463, 3, 143, 147), width = c(4, 1, 1, 765),
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_equal(start(res), c(1, -1, -1, -1))
expect_equal(end(res), c(4, -1, -1, -1))
txcoords <- IRanges(start = c(3, 143, 147), width = c(1, 1, 765),
names = c("ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_warning(res <- transcriptToCds(txcoords, edb18))
expect_true(all(start(res) < 0))
expect_true(all(end(res) < 0))
## Preloaded data test
exons <- exonsBy(edb18)
transcripts <- transcripts(edb18)
expect_error(transcriptToCds(db = edb18, exons = exons,transcripts = transcripts))
## 1) unknown tx ids
txcoords <- IRanges(start = c(4, 3), width = c(1, 1), names = c("a", "b"))
expect_error(transcriptToCds(x = txcoords))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_true(all(start(res) == -1))
expect_true(all(end(res) == -1))
## 2) all tx not coding
txcoords <- IRanges(start = c(132, 133), end = c(323, 323),
names = rep("ENST00000590515", 2))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_true(all(start(res) == -1))
expect_true(all(end(res) == -1))
## 3) some tx not coding
## 4) coordinate not within coding
txcoords <- IRanges(start = c(1463, 3, 143, 147, 1463), width = 1,
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955",
"ENST00000398117"))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_equal(start(res), c(1, -1, -1, 1, 1))
expect_equal(end(res), c(1, -1, -1, 1, 1))
expect_equal(res[1], res[5])
## End position outside of CDS
txcoords <- IRanges(start = c(1463, 3, 143, 147), width = c(4, 1, 1, 765),
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_equal(start(res), c(1, -1, -1, -1))
expect_equal(end(res), c(4, -1, -1, -1))
txcoords <- IRanges(start = c(3, 143, 147), width = c(1, 1, 765),
names = c("ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_warning(res <- transcriptToCds(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_true(all(start(res) < 0))
expect_true(all(end(res) < 0))
})
test_that("cdsToTranscript works", {
edb18 <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "18")
expect_error(cdsToTranscript())
expect_error(cdsToTranscript(db = edb18))
txcoords <- IRanges(start = c(4, 3, 143, 147), width = 1,
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_error(cdsToTranscript(x = txcoords))
expect_warning(res <- cdsToTranscript(txcoords, edb18))
expect_equal(start(res), c(1466, 902, -1, 293))
txcoords <- IRanges(start = c(4, 3, 50000, 147), width = 1,
names = c("ENST00000398117", "ENST00000398117",
"ENST00000398117", "b"))
expect_warning(res <- cdsToTranscript(txcoords, edb18))
expect_equal(start(res), c(1466, 1465, -1, -1))
## Map variants:
## ENST00000070846:c.1643DelG
## ENST00000070846:c.1881DelC
## ENST00000379802:c.6995C>A
## ENST00000261590:c.1088C>T
## ENST00000261590:c.561T>G
rngs <- IRanges(start = c(1643, 1881, 6995, 1088, 561), width = 1,
names = c("ENST00000070846", "ENST00000070846",
"ENST00000379802", "ENST00000261590",
"ENST00000261590"))
rngs_tx <- cdsToTranscript(rngs, EnsDb.Hsapiens.v86)
gnm <- transcriptToGenome(rngs_tx, EnsDb.Hsapiens.v86)
library(BSgenome.Hsapiens.NCBI.GRCh38)
res <- getSeq(BSgenome.Hsapiens.NCBI.GRCh38, unlist(gnm))
exp <- c("G", "C", "C", "C", "T")
expect_equal(exp, unname(as.character(res)))
## Preloaded data test
exons <- exonsBy(EnsDb.Hsapiens.v86)
transcripts <- transcripts(EnsDb.Hsapiens.v86)
edb18 <- filter(EnsDb.Hsapiens.v86, filter = ~ seq_name == "18")
expect_error(cdsToTranscript())
expect_error(cdsToTranscript(db = edb18, exons = exons,transcripts = transcripts))
txcoords <- IRanges(start = c(4, 3, 143, 147), width = 1,
names = c("ENST00000398117", "ENST00000333681",
"ENST00000590515", "ENST00000589955"))
expect_error(cdsToTranscript(x = txcoords))
expect_warning(res <- cdsToTranscript(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_equal(start(res), c(1466, 902, -1, 293))
txcoords <- IRanges(start = c(4, 3, 50000, 147), width = 1,
names = c("ENST00000398117", "ENST00000398117",
"ENST00000398117", "b"))
expect_warning(res <- cdsToTranscript(txcoords, edb18, exons = exons,transcripts = transcripts))
expect_equal(start(res), c(1466, 1465, -1, -1))
## Map variants:
## ENST00000070846:c.1643DelG
## ENST00000070846:c.1881DelC
## ENST00000379802:c.6995C>A
## ENST00000261590:c.1088C>T
## ENST00000261590:c.561T>G
rngs <- IRanges(start = c(1643, 1881, 6995, 1088, 561), width = 1,
names = c("ENST00000070846", "ENST00000070846",
"ENST00000379802", "ENST00000261590",
"ENST00000261590"))
rngs_tx <- cdsToTranscript(rngs, EnsDb.Hsapiens.v86, exons = exons,transcripts = transcripts)
gnm <- transcriptToGenome(rngs_tx, exons)
library(BSgenome.Hsapiens.NCBI.GRCh38)
res <- getSeq(BSgenome.Hsapiens.NCBI.GRCh38, unlist(gnm))
exp <- c("G", "C", "C", "C", "T")
expect_equal(exp, unname(as.character(res)))
})
test_that(".ids_message works", {
res <- .ids_message(c("a", "b"))
expect_equal(res, paste(c("a", "b"), collapse = ", "))
res <- .ids_message(c("a", "b", "c", "d", "e", "f"))
expect_equal(res, "a, b, c ... (3 more)")
expect_equal(.ids_message(c("c", "b", "c", "d")), "c, b, c ... (1 more)")
})
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