tests/testthat/test-loadPgExample.R

In FindMyFriends: Microbial Comparative Genomics in R

context("Example pangenome loading")

pgFull <- .loadPgExample()
pgLM <- .loadPgExample(lowMem=TRUE)
pgFullLoc <- .loadPgExample(geneLoc=TRUE)
pgLMLoc <- .loadPgExample(lowMem=TRUE, geneLoc=TRUE)
pgFullGr <- .loadPgExample(withGroups=TRUE)
pgLMGr <- .loadPgExample(lowMem=TRUE, withGroups=TRUE)
pgFullLocGr <- .loadPgExample(geneLoc=TRUE, withNeighborhoodSplit=TRUE)
pgLMLocGr <- .loadPgExample(lowMem=TRUE, geneLoc=TRUE, withNeighborhoodSplit=TRUE)
pgFullPara <- .loadPgExample(withGroups=TRUE, withParalogues=TRUE)
pgFullLocPara <- .loadPgExample(geneLoc=TRUE, withNeighborhoodSplit=TRUE, withParalogues=TRUE)
pgLMPara <- .loadPgExample(lowMem=TRUE, withGroups=TRUE, withParalogues=TRUE)
pgLMLocPara <- .loadPgExample(lowMem=TRUE, geneLoc=TRUE, withNeighborhoodSplit=TRUE, withParalogues=TRUE)

test_that("test object are correct class", {
    expect_is(pgFull, 'pgFull')
    expect_is(pgFullLoc, 'pgFull')
    expect_is(pgFullGr, 'pgFull')
    expect_is(pgFullLocGr, 'pgFull')
    expect_is(pgFullPara, 'pgFull')
    expect_is(pgFullLocPara, 'pgFull')
    expect_is(pgLM, 'pgLM')
    expect_is(pgLMLoc, 'pgLM')
    expect_is(pgLMGr, 'pgLM')
    expect_is(pgLMLocGr, 'pgLM')
    expect_is(pgLMPara, 'pgLM')
    expect_is(pgLMLocPara, 'pgLM')
    expect_is(pgFullLoc, 'pgFullLoc')
    expect_is(pgFullLocGr, 'pgFullLoc')
    expect_is(pgFullLocPara, 'pgFullLoc')
    expect_is(pgLMLoc, 'pgLMLoc')
    expect_is(pgLMLocGr, 'pgLMLoc')
    expect_is(pgLMLocPara, 'pgLMLoc')
})
test_that("test object contain the correct information", {
    expect_false(hasGeneGroups(pgFull))
    expect_false(hasGeneInfo(pgFull))
    expect_false(hasParalogueLinks(pgFull))
    
    expect_false(hasGeneGroups(pgLM))
    expect_false(hasGeneInfo(pgLM))
    expect_false(hasParalogueLinks(pgLM))
    
    expect_false(hasGeneGroups(pgFullLoc))
    expect_true(hasGeneInfo(pgFullLoc))
    expect_false(hasParalogueLinks(pgFullLoc))
    
    expect_false(hasGeneGroups(pgLMLoc))
    expect_true(hasGeneInfo(pgLMLoc))
    expect_false(hasParalogueLinks(pgLMLoc))
    
    expect_true(hasGeneGroups(pgFullGr))
    expect_false(hasGeneInfo(pgFullGr))
    expect_false(hasParalogueLinks(pgFullGr))
    
    expect_true(hasGeneGroups(pgLMGr))
    expect_false(hasGeneInfo(pgLMGr))
    expect_false(hasParalogueLinks(pgLMGr))
    
    expect_true(hasGeneGroups(pgFullLocGr))
    expect_true(hasGeneInfo(pgFullLocGr))
    expect_false(hasParalogueLinks(pgFullLocGr))
    
    expect_true(hasGeneGroups(pgLMLocGr))
    expect_true(hasGeneInfo(pgLMLocGr))
    expect_false(hasParalogueLinks(pgLMLocGr))
    
    expect_true(hasGeneGroups(pgFullPara))
    expect_false(hasGeneInfo(pgFullPara))
    expect_true(hasParalogueLinks(pgFullPara))
    
    expect_true(hasGeneGroups(pgFullLocPara))
    expect_true(hasGeneInfo(pgFullLocPara))
    expect_true(hasParalogueLinks(pgFullLocPara))
    
    expect_true(hasGeneGroups(pgLMPara))
    expect_false(hasGeneInfo(pgLMPara))
    expect_true(hasParalogueLinks(pgLMPara))
    
    expect_true(hasGeneGroups(pgLMLocPara))
    expect_true(hasGeneInfo(pgLMLocPara))
    expect_true(hasParalogueLinks(pgLMLocPara))
})