tests/testthat/test-prepareHLAdb.R
In NCBI-Hackathons/HLAClustRView: HLA typing clustering and visualization based on specific similarity metrics
### Unit tests for functions in prepareHLAdb.R file
library(HLAClustRView)
directory <- system.file("extdata", package = "HLAClustRView")
### Tests parseHLADbAlignment() results
context("parseHLADbAlignment() results")
test_that("parseHLADbAlignment() must return an error when directory is a number", {
message <- "The hlaDbPath parameter must by a character string"
expect_error(parseHLADbAlignment(hlaDbPath = 33, seqType = "nuc"), message)
})
test_that("parseHLADbAlignment() must return an error when no a valid sequence type", {
message <- "Not validate sequence type parameter for parseHLADbAlignment: toto"
expect_error(parseHLADbAlignment(hlaDbPath = directory, seqType = "toto"), message)
})
test_that("parseHLADbAlignment() must return an error when directory does not exist", {
path_to_test <- "./3_21_33eddger_39kdf_23sk2-2221fvd_qqqqqqqqqq_2"
if (!dir.exists(path_to_test)) {
message <- "The hlaDbPath parameter must by a valid directory"
expect_error(parseHLADbAlignment(hlaDbPath = path_to_test, seqType = "nuc"), message)
}
})
test_that("parseHLADbAlignment() must return an error when no file in directory", {
message <- "There must be at least one alignment file in the hlaDbPath directory"
expect_error(parseHLADbAlignment(hlaDbPath = directory, seqType = "nuc"), message)
})
#
# test_that("parseHLADbAlignment() must return an error when directory does not exist", {
# result <- parseHLADbAlignment(hlaDbPath = directory, seqType = "prot")
#
# expected <- list()
# expected[["refSeq"]] <- list()
# expected[["refSeq"]][['DOB']] <- paste0("NLTRLDSSMTQGTDSPEDFVIQAKADCYFTNGTEKVQFVVRFIFN",
# "LEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFY",
# "PGDIKIKWFLNGQEERAGVMSTGPIRNGDWTFQTVVMLEMTPELGHVRAQSEYSWRKMLSGIAAFLLGLIFL",
# "LVGIVIQLRAQKGYVRTQMSGNEVSRAVLLPQS")
# expected[["refSeq"]][['DRA']] <- paste0("IAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFH",
# "VDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLR",
# "NGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLTTENVVCALGLTVGLVGIIIGTIFI",
# "IKGVRKSNAAERRGPL")
# expected[["posInit"]] <- list()
# expected[["posInit"]][['DOB']] <- 171
# expected[["posInit"]][['DRA']] <- 171
#
# expected[["HLAAlignment"]] <- list()
#
#
# ## TODO
# })
context("extractTyping() results")
test_that("extractTyping() must return good result 01", {
sequence <- " DOB*01:01:01:02 MGSGWV PWVVALLVNL TRLDSSMTQG"
result <- HLAClustRView:::extractTyping(seq=sequence, endPos=20)
expected <- "DOB*01:01:01:02"
expect_equal(result, expected)
})
test_that("extractTyping() must return good result 02", {
sequence <- " MGSGWV PWVVALLVNL TRLDSSMTQG"
result <- HLAClustRView:::extractTyping(seq=sequence, endPos=20)
expected <- ""
expect_equal(result, expected)
})
context("extractRef() results")
test_that("extractRef() must return good result 01", {
sequence <- " DOB*01:01:01:01 MGSGWV PWVVALLVNL TRLDSSMTQG TDSPEDFVIQ AKADCYFTNG"
result <- HLAClustRView:::extractRef(seq=sequence, startPos=20)
expected <- list()
expected[["refSeq"]] <- " MGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTNG"
expected[["seqDiff"]] <- " ----------------------------------------------"
expect_equal(result, expected)
})
test_that("extractRef() must return good result 02", {
sequence <- " A*01:01:01:01 ATG GCC GTC ATG GCG CCC CGA ACC CTC CTC CTG CTA CTC TCG GGG "
result <- HLAClustRView:::extractRef(seq=sequence, startPos=21)
expected <- list()
expected[["refSeq"]] <- "TGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGG"
expected[["seqDiff"]] <- "--------------------------------------------"
expect_equal(result, expected)
})
context("extractSeq() results")
test_that("extractSeq() must return good result 01", {
sequence <- " F*01:06 --- --- --- --- --- --- --- --- --- -|-- "
result <- HLAClustRView:::extractSeq(seq=sequence, startPos=20)
expected <- "------------------------------"
expect_equal(result, expected)
})
test_that("extractSeq() must return good result 02", {
sequence <- " G*01:17 ----H----- --******** ********** ****"
result <- HLAClustRView:::extractSeq(seq=sequence, startPos=20)
expected <- "----H-------**********************"
expect_equal(result, expected)
})
context("getTypingPos() results")
test_that("getTypingPos() must return good result 01", {
seqData <- data.table(GeneName=rep("DOB", 3), AlleleGroup=rep("01", 3),
Protein=rep("01", 3), SynSubst=rep("01", 3),
Noncoding=c("01", "02", "03"), Suffix=rep(NA, 3))
typing <- matrix(data=c("DOB", "01", "01", "01", "03", NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 3
expect_equal(result, expected)
})
test_that("getTypingPos() must return good result 02", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=rep("01", 4),
Noncoding=c("01", "02", "03", "02"), Suffix=rep(NA, 4))
typing <- matrix(data=c("DOA", "01", "01", "01", "02", NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 4
expect_equal(result, expected)
})
test_that("getTypingPos() must return good result 03", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=rep("01", 4),
Noncoding=c("01", NA, "03", "02"), Suffix=c(NA, NA, "N", NA))
typing <- matrix(data=c("DOB", "01", "01", "01", NA, NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 2
expect_equal(result, expected)
})
test_that("getTypingPos() must return good result 04", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=rep("01", 4),
Noncoding=c("01", "02", "03", "02"), Suffix=c(NA, "N", "N", NA))
typing <- matrix(data=c("DOB", "01", "01", "01", "03", "N"), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 3
expect_equal(result, expected)
})
test_that("getTypingPos() must return good result 05", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=c(NA, "01", "01", NA),
Noncoding=c(NA, NA, "03", NA), Suffix=c(NA, NA, "N", NA))
typing <- matrix(data=c("DOA", "01", "01", NA, NA, NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 4
expect_equal(result, expected)
})
test_that("getTypingPos() must return NA when typing not present", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=rep("01", 4),
Noncoding=c("01", "02", "03", "02"), Suffix=rep(NA, 4))
typing <- matrix(data=c("DOA", "01", "01", "01", "03", NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- integer()
expect_equal(result, expected)
})
context("parseAlignment() results")
test_that("parseAlignment() must return good result 01", {
fileName <- paste0(directory, "/DRA_prot.txt")
result <- HLAClustRView:::parseAlignment(fileName = fileName)
expected <- list()
expected$refSeq <- paste0(" MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDF",
"DGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSP",
"VELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVE",
"HWGLDEPLLKHWEFDAPSPLPETTENVVCALGLTVGLVGIIIGTIFIIKGVRKSNAAERRGPL")
expected$posInit <- -30L
expected$HLAalignment <- data.table:::data.table(
GeneName = c(rep("DRA", 7), rep("", 4)), AlleleGroup = c(rep("01", 7), rep("", 4)),
Protein = c(rep("01", 4), rep("02", 3), rep("", 4)),
SynSubst = c(rep("01", 3), "02", "01", "02", "03", rep("", 4)),
Noncoding = c("01", "02", "03", rep(NA, 4), rep("", 4)),
Suffix = c(rep(NA, 7), rep("", 4)),
SeqDiff = c(rep(paste0(" ------------------------------------------------",
"------------------------------------------------------------------------",
"------------------------------------------------------------------------",
"--------------------------------------------------------------"), 4),
paste0(" ****************************---------------------------------------",
"------------------------------------------------------------------------",
"------------------------------------------------------------------------",
"------------------------------L------------"),
rep(paste0(" ---------------------------------------------------------------",
"--------------------------------------------------------------------",
"--------------------------------------------------------------------",
"------------------------------------------L------------"), 2),
rep("", 4)))
expect_true(is.list(result))
expect_equal(result, expected)
})
context("parseHLADbAlignment() results")
test_that("parseHLADbAlignment() must return good result 01", {
result <- parseHLADbAlignment(hlaDbPath = directory, seqType = "prot")
expected <- list()
refSeq <- list()
posInit <- list()
refSeq[["DOB"]] <- paste0(" MGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTNGTEKVQFVVRFIFNLEE",
"YVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVCRHNYRLGAPFTVGRKVQPEVTVYPERTP",
"LLHQHNLLHCSVTGFYPGDIKIKWFLNGQEERAGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHS",
"SLLSPVSVEWRAQSEYSWRKMLSGIAAFLLGLIFLLVGIVIQLRAQKGYVRTQMSGNEVSRAVLLPQSC")
refSeq[["DRA"]] <- paste0(" MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDF",
"DGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSP",
"VELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVE",
"HWGLDEPLLKHWEFDAPSPLPETTENVVCALGLTVGLVGIIIGTIFIIKGVRKSNAAERRGPL")
expected[["refSeq"]] <- refSeq
posInit[["DOB"]] <- -30L
posInit[["DRA"]] <- -30L
expected[["posInit"]] <- posInit
expected$HLAAlignment <- data.table:::data.table(
GeneName = c(rep("DOB", 13), rep("", 4), rep("DRA", 7), rep("", 4)),
AlleleGroup = c(rep("01", 13), rep("", 4), rep("01", 7), rep("", 4)),
Protein = c(rep("01", 7), rep("02", 2), "03", rep("04", 2), "05",
rep("", 4), rep("01", 4), rep("02", 3), rep("", 4)),
SynSubst = c(rep("01", 4), "02", rep("03", 2), "01", "02", NA,
rep("01", 2), NA, rep("", 4), rep("01", 3), "02", "01", "02", "03", rep("", 4)),
Noncoding = c(paste0("0", 1:4), NA, "01", "02", rep(NA, 3),
"01", "02", NA, rep("", 4), paste0("0", seq_len(3)), rep(NA, 4), rep("", 4)),
Suffix = c(rep(NA, 13), rep("", 4), rep(NA, 7), rep("", 4)),
SeqDiff = c(rep(paste0(" --------------------------------------------------------------------",
"-----------------------------------------------------------------------",
"-----------------------------------------------------------------------",
"---------------------------------------------------------------"), 7),
rep(paste0(" -----------------Q--------------------------------------------------",
"-----------------------------------------------------------------------",
"-----------------------------------------------------------------------",
"---------------------------------------------------------------"), 2),
paste0(" ------------------------------------------------------------------------",
"---------------------------------------------------------------------------",
"---------------------------------------------------------------------------",
"---------------------I-----------------------------"),
rep(paste0(" ----------------------------------------------------------------------",
"-------------------------------------------------------------------------",
"-------------------------------------------------------------------------",
"-----------------F---------------------------------------"), 2),
paste0(" --------------------------------------------------------------------------",
"------------------------------------------------------------------------------",
"-----------------------------------------------------",
"----I---------------------------------------------------------------"),
rep("", 4),
rep(paste0(" ------------------------------------------------",
"------------------------------------------------------------------------",
"------------------------------------------------------------------------",
"--------------------------------------------------------------"), 4),
paste0(" ****************************---------------------------------------",
"------------------------------------------------------------------------",
"------------------------------------------------------------------------",
"------------------------------L------------"),
rep(paste0(" ---------------------------------------------------------------",
"--------------------------------------------------------------------",
"--------------------------------------------------------------------",
"------------------------------------------L------------"), 2),
rep("", 4)))
class(expected) <- "HLAdb"
expect_true(is.list(result))
expect_equal(result, expected)
})
NCBI-Hackathons/HLAClustRView documentation built on Nov. 22, 2019, 6:11 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
### Unit tests for functions in prepareHLAdb.R file
library(HLAClustRView)
directory <- system.file("extdata", package = "HLAClustRView")
### Tests parseHLADbAlignment() results
context("parseHLADbAlignment() results")
test_that("parseHLADbAlignment() must return an error when directory is a number", {
message <- "The hlaDbPath parameter must by a character string"
expect_error(parseHLADbAlignment(hlaDbPath = 33, seqType = "nuc"), message)
})
test_that("parseHLADbAlignment() must return an error when no a valid sequence type", {
message <- "Not validate sequence type parameter for parseHLADbAlignment: toto"
expect_error(parseHLADbAlignment(hlaDbPath = directory, seqType = "toto"), message)
})
test_that("parseHLADbAlignment() must return an error when directory does not exist", {
path_to_test <- "./3_21_33eddger_39kdf_23sk2-2221fvd_qqqqqqqqqq_2"
if (!dir.exists(path_to_test)) {
message <- "The hlaDbPath parameter must by a valid directory"
expect_error(parseHLADbAlignment(hlaDbPath = path_to_test, seqType = "nuc"), message)
}
})
test_that("parseHLADbAlignment() must return an error when no file in directory", {
message <- "There must be at least one alignment file in the hlaDbPath directory"
expect_error(parseHLADbAlignment(hlaDbPath = directory, seqType = "nuc"), message)
})
#
# test_that("parseHLADbAlignment() must return an error when directory does not exist", {
# result <- parseHLADbAlignment(hlaDbPath = directory, seqType = "prot")
#
# expected <- list()
# expected[["refSeq"]] <- list()
# expected[["refSeq"]][['DOB']] <- paste0("NLTRLDSSMTQGTDSPEDFVIQAKADCYFTNGTEKVQFVVRFIFN",
# "LEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFY",
# "PGDIKIKWFLNGQEERAGVMSTGPIRNGDWTFQTVVMLEMTPELGHVRAQSEYSWRKMLSGIAAFLLGLIFL",
# "LVGIVIQLRAQKGYVRTQMSGNEVSRAVLLPQS")
# expected[["refSeq"]][['DRA']] <- paste0("IAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFH",
# "VDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLR",
# "NGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLTTENVVCALGLTVGLVGIIIGTIFI",
# "IKGVRKSNAAERRGPL")
# expected[["posInit"]] <- list()
# expected[["posInit"]][['DOB']] <- 171
# expected[["posInit"]][['DRA']] <- 171
#
# expected[["HLAAlignment"]] <- list()
#
#
# ## TODO
# })
context("extractTyping() results")
test_that("extractTyping() must return good result 01", {
sequence <- " DOB*01:01:01:02 MGSGWV PWVVALLVNL TRLDSSMTQG"
result <- HLAClustRView:::extractTyping(seq=sequence, endPos=20)
expected <- "DOB*01:01:01:02"
expect_equal(result, expected)
})
test_that("extractTyping() must return good result 02", {
sequence <- " MGSGWV PWVVALLVNL TRLDSSMTQG"
result <- HLAClustRView:::extractTyping(seq=sequence, endPos=20)
expected <- ""
expect_equal(result, expected)
})
context("extractRef() results")
test_that("extractRef() must return good result 01", {
sequence <- " DOB*01:01:01:01 MGSGWV PWVVALLVNL TRLDSSMTQG TDSPEDFVIQ AKADCYFTNG"
result <- HLAClustRView:::extractRef(seq=sequence, startPos=20)
expected <- list()
expected[["refSeq"]] <- " MGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTNG"
expected[["seqDiff"]] <- " ----------------------------------------------"
expect_equal(result, expected)
})
test_that("extractRef() must return good result 02", {
sequence <- " A*01:01:01:01 ATG GCC GTC ATG GCG CCC CGA ACC CTC CTC CTG CTA CTC TCG GGG "
result <- HLAClustRView:::extractRef(seq=sequence, startPos=21)
expected <- list()
expected[["refSeq"]] <- "TGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGG"
expected[["seqDiff"]] <- "--------------------------------------------"
expect_equal(result, expected)
})
context("extractSeq() results")
test_that("extractSeq() must return good result 01", {
sequence <- " F*01:06 --- --- --- --- --- --- --- --- --- -|-- "
result <- HLAClustRView:::extractSeq(seq=sequence, startPos=20)
expected <- "------------------------------"
expect_equal(result, expected)
})
test_that("extractSeq() must return good result 02", {
sequence <- " G*01:17 ----H----- --******** ********** ****"
result <- HLAClustRView:::extractSeq(seq=sequence, startPos=20)
expected <- "----H-------**********************"
expect_equal(result, expected)
})
context("getTypingPos() results")
test_that("getTypingPos() must return good result 01", {
seqData <- data.table(GeneName=rep("DOB", 3), AlleleGroup=rep("01", 3),
Protein=rep("01", 3), SynSubst=rep("01", 3),
Noncoding=c("01", "02", "03"), Suffix=rep(NA, 3))
typing <- matrix(data=c("DOB", "01", "01", "01", "03", NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 3
expect_equal(result, expected)
})
test_that("getTypingPos() must return good result 02", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=rep("01", 4),
Noncoding=c("01", "02", "03", "02"), Suffix=rep(NA, 4))
typing <- matrix(data=c("DOA", "01", "01", "01", "02", NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 4
expect_equal(result, expected)
})
test_that("getTypingPos() must return good result 03", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=rep("01", 4),
Noncoding=c("01", NA, "03", "02"), Suffix=c(NA, NA, "N", NA))
typing <- matrix(data=c("DOB", "01", "01", "01", NA, NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 2
expect_equal(result, expected)
})
test_that("getTypingPos() must return good result 04", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=rep("01", 4),
Noncoding=c("01", "02", "03", "02"), Suffix=c(NA, "N", "N", NA))
typing <- matrix(data=c("DOB", "01", "01", "01", "03", "N"), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 3
expect_equal(result, expected)
})
test_that("getTypingPos() must return good result 05", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=c(NA, "01", "01", NA),
Noncoding=c(NA, NA, "03", NA), Suffix=c(NA, NA, "N", NA))
typing <- matrix(data=c("DOA", "01", "01", NA, NA, NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- 4
expect_equal(result, expected)
})
test_that("getTypingPos() must return NA when typing not present", {
seqData <- data.table(GeneName=c(rep("DOB", 3), "DOA"), AlleleGroup=rep("01", 4),
Protein=rep("01", 4), SynSubst=rep("01", 4),
Noncoding=c("01", "02", "03", "02"), Suffix=rep(NA, 4))
typing <- matrix(data=c("DOA", "01", "01", "01", "03", NA), nrow=1)
result <- HLAClustRView:::getTypingPos(seqProcess=seqData, curTyping=typing)
expected <- integer()
expect_equal(result, expected)
})
context("parseAlignment() results")
test_that("parseAlignment() must return good result 01", {
fileName <- paste0(directory, "/DRA_prot.txt")
result <- HLAClustRView:::parseAlignment(fileName = fileName)
expected <- list()
expected$refSeq <- paste0(" MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDF",
"DGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSP",
"VELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVE",
"HWGLDEPLLKHWEFDAPSPLPETTENVVCALGLTVGLVGIIIGTIFIIKGVRKSNAAERRGPL")
expected$posInit <- -30L
expected$HLAalignment <- data.table:::data.table(
GeneName = c(rep("DRA", 7), rep("", 4)), AlleleGroup = c(rep("01", 7), rep("", 4)),
Protein = c(rep("01", 4), rep("02", 3), rep("", 4)),
SynSubst = c(rep("01", 3), "02", "01", "02", "03", rep("", 4)),
Noncoding = c("01", "02", "03", rep(NA, 4), rep("", 4)),
Suffix = c(rep(NA, 7), rep("", 4)),
SeqDiff = c(rep(paste0(" ------------------------------------------------",
"------------------------------------------------------------------------",
"------------------------------------------------------------------------",
"--------------------------------------------------------------"), 4),
paste0(" ****************************---------------------------------------",
"------------------------------------------------------------------------",
"------------------------------------------------------------------------",
"------------------------------L------------"),
rep(paste0(" ---------------------------------------------------------------",
"--------------------------------------------------------------------",
"--------------------------------------------------------------------",
"------------------------------------------L------------"), 2),
rep("", 4)))
expect_true(is.list(result))
expect_equal(result, expected)
})
context("parseHLADbAlignment() results")
test_that("parseHLADbAlignment() must return good result 01", {
result <- parseHLADbAlignment(hlaDbPath = directory, seqType = "prot")
expected <- list()
refSeq <- list()
posInit <- list()
refSeq[["DOB"]] <- paste0(" MGSGWVPWVVALLVNLTRLDSSMTQGTDSPEDFVIQAKADCYFTNGTEKVQFVVRFIFNLEE",
"YVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVCRHNYRLGAPFTVGRKVQPEVTVYPERTP",
"LLHQHNLLHCSVTGFYPGDIKIKWFLNGQEERAGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHS",
"SLLSPVSVEWRAQSEYSWRKMLSGIAAFLLGLIFLLVGIVIQLRAQKGYVRTQMSGNEVSRAVLLPQSC")
refSeq[["DRA"]] <- paste0(" MAISGVPVLGFFIIAVLMSAQESWAIKEEHVIIQAEFYLNPDQSGEFMFDF",
"DGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSP",
"VELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVE",
"HWGLDEPLLKHWEFDAPSPLPETTENVVCALGLTVGLVGIIIGTIFIIKGVRKSNAAERRGPL")
expected[["refSeq"]] <- refSeq
posInit[["DOB"]] <- -30L
posInit[["DRA"]] <- -30L
expected[["posInit"]] <- posInit
expected$HLAAlignment <- data.table:::data.table(
GeneName = c(rep("DOB", 13), rep("", 4), rep("DRA", 7), rep("", 4)),
AlleleGroup = c(rep("01", 13), rep("", 4), rep("01", 7), rep("", 4)),
Protein = c(rep("01", 7), rep("02", 2), "03", rep("04", 2), "05",
rep("", 4), rep("01", 4), rep("02", 3), rep("", 4)),
SynSubst = c(rep("01", 4), "02", rep("03", 2), "01", "02", NA,
rep("01", 2), NA, rep("", 4), rep("01", 3), "02", "01", "02", "03", rep("", 4)),
Noncoding = c(paste0("0", 1:4), NA, "01", "02", rep(NA, 3),
"01", "02", NA, rep("", 4), paste0("0", seq_len(3)), rep(NA, 4), rep("", 4)),
Suffix = c(rep(NA, 13), rep("", 4), rep(NA, 7), rep("", 4)),
SeqDiff = c(rep(paste0(" --------------------------------------------------------------------",
"-----------------------------------------------------------------------",
"-----------------------------------------------------------------------",
"---------------------------------------------------------------"), 7),
rep(paste0(" -----------------Q--------------------------------------------------",
"-----------------------------------------------------------------------",
"-----------------------------------------------------------------------",
"---------------------------------------------------------------"), 2),
paste0(" ------------------------------------------------------------------------",
"---------------------------------------------------------------------------",
"---------------------------------------------------------------------------",
"---------------------I-----------------------------"),
rep(paste0(" ----------------------------------------------------------------------",
"-------------------------------------------------------------------------",
"-------------------------------------------------------------------------",
"-----------------F---------------------------------------"), 2),
paste0(" --------------------------------------------------------------------------",
"------------------------------------------------------------------------------",
"-----------------------------------------------------",
"----I---------------------------------------------------------------"),
rep("", 4),
rep(paste0(" ------------------------------------------------",
"------------------------------------------------------------------------",
"------------------------------------------------------------------------",
"--------------------------------------------------------------"), 4),
paste0(" ****************************---------------------------------------",
"------------------------------------------------------------------------",
"------------------------------------------------------------------------",
"------------------------------L------------"),
rep(paste0(" ---------------------------------------------------------------",
"--------------------------------------------------------------------",
"--------------------------------------------------------------------",
"------------------------------------------L------------"), 2),
rep("", 4)))
class(expected) <- "HLAdb"
expect_true(is.list(result))
expect_equal(result, expected)
})
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.