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test_3_extract_gt.R
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test_3_extract_gt.R
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# extractgt devel
#
library(testthat)
#detach(package:vcfR, unload=TRUE)
library(vcfR)
context("extract.gt functions")
#
data(vcfR_example)
#vcf_file <- system.file("extdata", "pinf_sc1_100_sub.vcf.gz", package = "vcfR")
#seq_file <- system.file("extdata", "pinf_sc100.fasta", package = "vcfR")
#gff_file <- system.file("extdata", "pinf_sc100.gff", package = "vcfR")
#vcf <- read.vcfR(vcf_file, verbose = FALSE)
#dna <- ape::read.dna(seq_file, format = "fasta")
#gff <- read.table(gff_file, sep="\t")
chrom <- create.chromR(name="Chrom", vcf=vcf, seq=dna, ann=gff, verbose=FALSE)
chrom <- masker(chrom, min_DP = 1e3, max_DP = 2e3)
##### ##### ##### ##### #####
gt <- extract.gt(chrom, element="GT", as.numeric=FALSE)
gt2 <- extract.gt(chrom, element="GT", as.numeric=FALSE, mask = TRUE)
gt3 <- extract.gt(chrom, element="GT", mask = c(TRUE, FALSE)) # Recycled vector
pl <- extract.gt(chrom, element="PL", as.numeric=FALSE)
gq <- extract.gt(chrom, element="GQ", as.numeric=TRUE)
##### ##### ##### ##### #####
#
# extract.gt tests
#
##### ##### ##### ##### #####
test_that("gt, pl ad gq are matrices",{
expect_is(gt, "matrix")
expect_is(gt2, "matrix")
expect_is(pl, "matrix")
expect_is(gq, "matrix")
})
test_that("gq is numeric",{
expect_is(gq, "matrix")
expect_equal(is.numeric(gq), TRUE)
})
test_that("extract.gt mask=TRUE works", {
expect_equal(nrow(gt), nrow(vcf@gt))
expect_equal(nrow(gt2), sum(chrom@var.info$mask))
expect_equal(nrow(gt3), nrow(gt[c(TRUE, FALSE),]))
})
test_that("extract.gt extract parameter works",{
gt <- extract.gt(chrom, element="GT", extract=TRUE)
expect_is(gq, "matrix")
expect_equal(is.numeric(gq), TRUE)
})
##### ##### ##### ##### #####
#
# extract.gt missing data.
#
##### ##### ##### ##### #####
test_that("extract.gt converts missing GT to NA",{
data("vcfR_test")
vcfR_test@gt[1,2] <- "./.:48:1:51,51"
gt <- extract.gt(vcfR_test)
expect_true( is.na(gt[1,1]) )
vcfR_test@gt[1,2] <- ".|.:48:1:51,51"
gt <- extract.gt(vcfR_test)
expect_true( is.na(gt[1,1]) )
vcfR_test@gt[1,2] <- ".|0:48:1:51,51"
gt <- extract.gt(vcfR_test)
expect_false( is.na(gt[1,1]) )
})
test_that("extract.gt convertNA = FALSE works",{
data("vcfR_test")
vcfR_test@gt[1,2] <- "./.:48:1:51,51"
gt <- extract.gt(vcfR_test, convertNA = FALSE)
expect_false( is.na( gt[1,1] ) )
vcfR_test@gt[1,2] <- ".|.:48:1:51,51"
gt <- extract.gt(vcfR_test, convertNA = FALSE)
expect_false( is.na(gt[1,1]) )
})
##### ##### ##### ##### #####
#
# extract.gt return.alleles tests
#
##### ##### ##### ##### #####
#alleles <- .Call('vcfR_gt2alleles', PACKAGE = 'vcfR', "0|1", c("T","C"))
#alleles <- .Call('vcfR_gt2alleles', PACKAGE = 'vcfR', "0|1", c("ATATTTAAACTTGCCAGTT","A"))
test_that("extract.gt return.alleles works #1",{
data(vcfR_test)
gt <- extract.gt(vcfR_test, element="GT")
gt <- extract.gt(vcfR_test, element="GT", return.alleles=TRUE)
expect_is(gt, "matrix")
})
test_that("extract.gt return.alleles works #2",{
data(vcfR_example)
# gt <- extract.gt(vcf, element="GT")
# gt <- extract.gt(vcf[430:438,], element="GT", return.alleles=TRUE)
# gt <- extract.gt(vcf[430:439,], element="GT", return.alleles=TRUE)
# GT = 0|0
# allele_vector = c("T","C")
gt <- extract.gt(vcf[438,1:2], element="GT", return.alleles=TRUE)
# GT = 0|0
# allele_vector = c("ATATTTAAACTTGCCAGTT", "A")
gt <- extract.gt(vcf[439,1:2], element="GT", return.alleles=TRUE)
expect_is(gt, "matrix")
})
# This is my stack overflow.
test_that("extract.gt return.alleles works",{
gt <- extract.gt(chrom,
element="GT",
return.alleles = TRUE
# allele.sep="|"
)
expect_is(gt, "matrix")
})
test_that("extract.gt return.alleles works for multiallelic variants",{
# vcf2 <- vcf[nchar(vcf@fix[,'ALT']) > 1,]
vcf2 <- vcf[grep(",", vcf@fix[,'ALT']),]
gt <- extract.gt(vcf2,
element="GT",
return.alleles = TRUE
# allele.sep="|"
)
# Locus 1: 0,1,2 = T,A,G
# 0|0
expect_equal( as.character(gt[1,'BL2009P4_us23']), "T|T")
# 0|1
expect_equal( as.character(gt[1,'DDR7602']), "T|A")
# 0|2
expect_equal( as.character(gt[1,'blue13']), "T|G")
# Locus 6: 0,1,2 = G,GTCTAATAGAGGCTCGAACTC,GTCTAATAGAGGCTCGAGCTC
# 0|2
expect_equal( as.character(gt[6,'BL2009P4_us23']), "G|GTCTAATAGAGGCTCGAGCTC")
# 1|2
expect_equal( as.character(gt[6,'DDR7602']), "GTCTAATAGAGGCTCGAACTC|GTCTAATAGAGGCTCGAGCTC" )
})
##### ##### ##### ##### #####
#
# extract.haps tests
#
##### ##### ##### ##### #####
data(vcfR_example)
gt <- extract.gt(vcf, element="GT", extract=TRUE)
test_that("extract_haps compiled code works",{
is.na(gt[1:5,1]) <- TRUE
gt[1:5,2] <- ".|."
gt[4,2] <- "0|."
gt[5,2] <- ".|1"
haps <- .Call('vcfR_extract_haps', PACKAGE = 'vcfR', vcf@fix[,'REF'], vcf@fix[,'ALT'], gt, 0, 0)
expect_is(haps, "matrix")
expect_true( is.na(haps[1,1]) )
expect_true( is.na(haps[1,2]) )
expect_true( is.na(haps[1,3]) )
expect_true( is.na(haps[1,4]) )
expect_true( !is.na(haps[4,3]) )
expect_true( is.na(haps[4,4]) )
expect_true( is.na(haps[5,3]) )
expect_true( !is.na(haps[5,4]) )
expect_equal(ncol(haps), 2 * ncol(gt))
expect_equal(nrow(haps), nrow(gt))
})
test_that("extract_haps R code works on vcfR objects",{
vcf@gt[1,3] <- ".|.:12,0:12:39:0,39,585"
vcf@gt[2,3] <- "0|.:12,0:12:39:0,39,585"
vcf@gt[3,3] <- ".|1:12,0:12:39:0,39,585"
haps <- extract.haps(vcf, verbose = FALSE)
haps[1:6,1:8]
expect_true( is.na(haps[1,3]) )
expect_true( is.na(haps[1,4]) )
expect_true( !is.na(haps[2,3]) )
expect_true( is.na(haps[2,4]) )
expect_true( is.na(haps[3,3]) )
expect_true( !is.na(haps[3,4]) )
})
chrom <- create.chromR(name="Chrom", vcf=vcf, seq=dna, ann=gff, verbose=FALSE)
chrom <- masker(chrom, min_DP = 1e3, max_DP = 2e3)
test_that("extract_haps R code works on chromR objects",{
haps <- extract.haps(chrom, verbose = FALSE)
expect_is(haps, "matrix")
expect_equal(ncol(haps), 2 * ncol(gt))
expect_equal(nrow(haps), nrow(gt))
})
test_that("extract_haps unphased_as_NA works",{
data(vcfR_test)
haps <- extract.haps(vcfR_test, unphased_as_NA = FALSE, verbose = FALSE)
expect_equal(sum(is.na(haps)), 0)
haps <- extract.haps(vcfR_test, unphased_as_NA = TRUE, verbose = FALSE)
expect_equal(sum(is.na(haps)), 14)
})
##### ##### ##### ##### #####
#
# extract.indels tests
#
##### ##### ##### ##### #####
test_that("extract.indels works",{
indels <- extract.indels(vcf, return.indels=TRUE)
expect_equal(nrow(indels@fix), 328)
})
##### ##### ##### ##### #####
#
# gt2alleles tests
#
##### ##### ##### ##### #####
#data(vcfR_example)
#vcf <- vcf[1:4, 1:3]
#vcf@gt[2,3] <- ".|0:12,0:12:39:0,39,585"
#vcf@gt[3,3] <- "0|.:12,0:12:39:0,39,585"
#vcf@gt[4,3] <- ".|.:12,0:12:39:0,39,585"
test_that("gt2alleles works",{
data("vcfR_test")
vcfR_test@gt
gt <- extract.gt(vcfR_test, return.alleles=TRUE)
# gt
expect_equal( as.character(gt[1,1]), "G|G")
expect_equal( as.character(gt[1,3]), "A/A")
expect_equal( as.character(gt[5,1]), "GTC/G")
# cbind(vcf@fix[,4:5], vcf@gt)
# gt <- extract.gt(vcf, return.alleles=TRUE, allele.sep = "|")
# expect_equal( as.character(gt[1,2]), "T|T")
# expect_equal( as.character(gt[2,2]), ".|C")
# expect_equal( as.character(gt[3,2]), "A|.")
# expect_equal( as.character(gt[4,2]), ".|.")
})
##### ##### ##### ##### #####
#
#
#
##### ##### ##### ##### #####
test_that("extract_gt_to_CM2 compiled code works",{
gt <- .Call( 'vcfR_extract_GT_to_CM2', PACKAGE = 'vcfR',
fix = vcf@fix, gt = vcf@gt,
element = 'GT',
alleles = 0, extract = 1, convertNA = 1 )
# head(gt)
# Return alleles
gt <- .Call( 'vcfR_extract_GT_to_CM2', PACKAGE = 'vcfR',
fix = vcf@fix, gt = vcf@gt,
element = 'GT',
alleles = 1, extract = 1, convertNA = 1 )
# head(gt)
gt <- .Call( 'vcfR_extract_GT_to_CM2', PACKAGE = 'vcfR',
fix = vcf@fix, gt = vcf@gt,
element = 'DP',
alleles = 0, extact = 1, convertNA = 1 )
# head(gt)
# Manage NA_STRING
# grep("\\.", gt[,1], value = TRUE)
expect_equal(length( grep("\\.", gt) ), 0)
})
##### ##### ##### ##### #####
##### ##### ##### ##### #####
#
# extract.info tests
#
##### ##### ##### ##### #####
test_that("extract.info handles missing elements",{
data(vcfR_test)
# Element is present in some, but not all, samples.
info <- extract.info(vcfR_test, element = "AF")
expect_equal(length(info), nrow(vcfR_test))
expect_equal( length(grep("AF", vcfR_test@fix[,'INFO'])), sum( !is.na(info) ) )
# Element does not exist.
info <- extract.info(vcfR_test, element = "XX")
expect_equal( length(grep("XX", vcfR_test@fix[,'INFO'])), sum( !is.na(info) ) )
})
##### ##### ##### ##### #####
# EOF.