tests/testthat/test-all.R

In Tasu/EpDB2UG: Utilities to work with EupathDB and UGENE

#testthat test
context(paste("test for refactoring, output file should be consistent, test working dir is", getwd()))
cat("\nloading \"tools\" package for md5sum\n")
library(tools)#for md5 check, only for testthat
#####
test_that("legacy", {
  input<-"./testdata/input/"
  checksumExpect<-md5sum(files = "./testdata/expect/testTGME49_chrX_1032284_1067339.gff3.gb")
  #test
  toxodb2ugene("./testdata/input/testTGME49_chrX_1032284_1067339.gff3")
  checksupTest<-md5sum("./testdata/input/testTGME49_chrX_1032284_1067339.gff3.gb")
  fs<-dir(input)
  fs<-paste(input,fs[!grepl("gff3$",fs)],sep="")
  file.remove(fs)
  expect_that(as.character(checksupTest[1]), equals(as.character(checksumExpect[1])))
})

test_that("no temp file", {
  input<-"./testdata/input/"
  checksumExpect<-md5sum(files = "./testdata/expect/testTGME49_chrX_1032284_1067339.gff3.gb")
  #test
  inputGFF3OutputGenbank("./testdata/input/testTGME49_chrX_1032284_1067339.gff3")
  checksupTest<-md5sum("./testdata/input/testTGME49_chrX_1032284_1067339.gff3.gb")
  fs<-dir(input)
  fs<-paste(input,fs[!grepl("gff3$",fs)],sep="")
  file.remove(fs)
  expect_that(as.character(checksupTest[1]), equals(as.character(checksumExpect[1])))
})

test_that("get gLocus from GeneID", {
  geneOfInterest<-"TGME49_286470"
  gff<-"./testdata/current-toxodb/ToxoDB-28_TgondiiME49.gff"
  time0<-Sys.time()
  gLocus<-findGeneLocusFromToxoDBGFF(geneId=geneOfInterest,gff=gff)
  time1<-Sys.time()
  gLocus2<-loadAllOnMemotry(geneId=geneOfInterest,gff=gff)
  time2<-Sys.time()
  cat(paste("\nline by line / read file at once; ", difftime(time1,time0),difftime(time2,time1)))
  expect_that(gLocus, equals(gLocus<-readRDS("./testdata/expect/TGME49_286470-gLocus.rds")))
  expect_that(gLocus2, equals(gLocus<-readRDS("./testdata/expect/TGME49_286470-gLocus.rds")))
})