# THESE TESTS WILL ONLY WORK ON MY LOCAL MACHINE #
#
# alignmentDir = file.path("/Users/milchevs/ownCloud/ProbeRemapStep3/R/testdata/DroGene1_1/", "Alignments")
# # alignmentDir = "/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/MoGene2/"
# load("/Users/milchevs/Downloads/NewPackages/DroGene1_1/dmel-all-r6.09.gtf.AnnotationDataFrame.RData") # Annotation
# # load("/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/Annotations/AnnotationDataFrame.Mus_musculus.GRCm38.82.RData")
# # load the alignments
# options(stringsAsFactors = FALSE)
#
#
#
# #load("8apr2016.RData")
#
# ########### PGF ###############################################
# alignmentDir = "/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/MoGene2/"
# load("/Users/milchevs/Documents/Biology/PROJECTS/Paul_Bertone/ReANNot/Annotations/AnnotationDataFrame.Mus_musculus.GRCm38.82.RData")
# dir1 = "/Users/milchevs/ownCloud/ProbeRemapSteps14/inst/extdata/mogene2_affyLibFiles_pgfBased/"
# outDir = "./tmpDRO/"
# o1 = makeOriginalPackageObject(originalAnnotationDir = dir1, organism = "Mouse", species = "Mus musculus", outputDir = outDir )
#
# undebug(alignments2parsedData)
#
# NEW_PD = alignments2parsedData(alignment.dir = alignmentDir,
# Annotation = ANN_MUS_all,
# outputDir = outDir,
# level = "gene",
# min_probe_number = 1,
# package_seed = o1)
#
# test_that("New Parsed Data corresponds to the array format (PGF)",
# {
# if(o1[[3]] == "pgf")
# {
# expect_true(length(NEW_PD) == 10)
# expect_true(setequal(names(NEW_PD), c("featureSet", "pmFeatures", "mmFeatures", "geometry", "pmSequence",
# "mmSequence", "chrom_dict", "level_dict", "type_dict", "core")))
# }
# })
#
####
# test_that("Error when wrong inputs",
# {
# expect_error(alignments2parsedData(alignment.dir = tempdir(), # dir does not contain what is needed
# Annotation = ANN_MUS_all,
# outputDir = outDir,
# level = "gene",
# min_probe_number = 1,
# package_seed = o1), regexp = "Wrong alignment directory")
# # generate wrong annotation table #
# Annot_wrong = subset(ANN_MUS_all, feature == "exon")
# expect_error(alignments2parsedData(alignment.dir = alignmentDir,
# Annotation = Annot_wrong, # Annotation does not contain feature like transcript or RNA
# outputDir = outDir,
# level = "gene",
# min_probe_number = 1,
# package_seed = o1), regexp = "transcript|RNA")
#
# expect_error(alignments2parsedData(alignment.dir = alignmentDir,
# Annotation = ANN_MUS_all,
# outputDir = "./outDir/nonexisting/path/", #non existing path to output directory
# level = "gene",
# min_probe_number = 1,
# package_seed = o1), regexp = "outputDir")
#
# expect_error(alignments2parsedData(alignment.dir = alignmentDir,
# Annotation = ANN_MUS_all,
# outputDir = outDir,
# level = "ggene", # typo in level
# min_probe_number = 1,
# package_seed = o1), regexp = "level")
#
# expect_error(alignments2parsedData(alignment.dir = alignmentDir,
# Annotation = ANN_MUS_all,
# outputDir = outDir,
# level = "gene",
# min_probe_number = 0,
# package_seed = o1), regexp = "min_probe_number")
#
# expect_error(alignments2parsedData(alignment.dir = alignmentDir,
# Annotation = ANN_MUS_all,
# outputDir = outDir,
# level = "gene",
# min_probe_number = 1,
# package_seed = "?"), # wrong package_seed input
# regexp = "package_seed")
#
#
# })
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