tests/testthat/test-cdsfile2rbh.R

In kullrich/CRBHits: Conditional reciprocal best hits (CRBHits) in R

test_that("cdsfile2rbh() outputs correct number of conditional reciprocal best hit pairs", {
    #CRBHits_root <- system.file(package="CRBHits")
    #LastTempDir <- tempdir()
    #system(paste0("unzip -o ", CRBHits_root, "/extdata/last-1542.zip -d ",
    #LastTempDir))
    #system(paste0("cd ", LastTempDir, "/last-1542/; make"))
    tmp.paths <- CRBHits::make_vignette()
    athfile <- system.file("fasta/ath.cds.fasta.gz", package="CRBHits")
    alyfile <- system.file("fasta/aly.cds.fasta.gz", package="CRBHits")
    #ath_aly_crbh <- cdsfile2rbh(athfile, alyfile,
    #lastpath=paste0(LastTempDir, "/last-1542/bin/"))
    ath_aly_crbh <- cdsfile2rbh(athfile, alyfile, lastpath=tmp.paths[1])
    expect_equal(dim(ath_aly_crbh$crbh.pairs)[1], 211)
})