context("import function for file import")
library(rseAnalysis)
test_that("vcf2df file loading", {
#non present folder
expect_error(vcf <- vcf2df("./foo/test.vcf"))
#corrupted file path
expect_error(vcf <- vcf2df("\test.vcf"))
#corrupted file type
expect_error(vcf <- vcf2df("./tests/source/test.vff"))
filePath <- system.file("extdata", "test.vcf", package = "rseAnalysis")
vcf <- vcf2df(filePath)
#check for result type
expect_match(typeof(vcf$CHROM), "character")
expect_match(typeof(vcf$POS), "integer")
expect_match(typeof(vcf$ID), "character")
expect_match(typeof(vcf$REF), "character")
expect_match(typeof(vcf$ALT), "character")
expect_match(typeof(vcf$CONSEQUENCE), "character")
expect_match(typeof(vcf$OCCURRENCE), "character")
expect_match(typeof(vcf$affected_donors), "integer")
expect_match(typeof(vcf$project_count), "integer")
})
test_that("fasta2df file loading", {
#non present folder
expect_error(fasta <- fasta2df("./foo/test.fasta"))
#corrupted file path
expect_error(fasta <- fasta2df("\test.fasta"))
#corrupted file type
expect_error(fasta <- fasta2df("./tests/source/test.fastaaa"))
filePath <- system.file("extdata", "test.fasta", package = "rseAnalysis")
fasta <- fasta2df(filePath)
#check for result type
expect_match(typeof(fasta$NAME), "character")
expect_match(typeof(fasta$SEQ), "character")
})
test_that("bed2df file loading", {
#non present folder
expect_error(bed <- bed2df("./foo/test.bed"))
#corrupted file path
expect_error(bed <- bed2df("\test.bed"))
#corrupted file type
expect_error(bed <- bed2df("./tests/source/test.beeed"))
filePath <- system.file("extdata", "test.bed", package = "rseAnalysis")
bed <- bed2df(filePath)
#check for result type
expect_match(typeof(bed$CHROM), "character")
expect_match(typeof(bed$STAPOS), "integer")
expect_match(typeof(bed$ENDPOS), "integer")
expect_match(typeof(bed$DIR), "character")
expect_match(typeof(bed$TYPE), "character")
expect_match(typeof(bed$ID), "character")
expect_match(typeof(bed$ALIAS), "character")
expect_match(typeof(bed$NAME), "character")
})
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