tests/testthat/test_mgDb-select.R

In metagenomeFeatures: Exploration of marker-gene sequence taxonomic annotations

context("mgDb-select")

## Select Methods
test_that("MgDb-class select arguments",{
    expect_error(mgDb_select(testMgDb, type = "not a type"))
    expect_error(mgDb_select(testMgDb, type = "all", keytype = "Keys"))
    expect_error(mgDb_select(testMgDb, type = "all", keys = "Streptomyces"))
})

## Test select will fail for seqs as the seq slot contains a different representation, seqDB than the select returns, DNAStringSet.
##
## Removing Decipher columns
test_taxa_df <- dplyr::collect(testMgDb@taxa)
test_taxa_df$row_names <- NULL
test_taxa_df$description <- NULL
test_taxa_df$identifier <- NULL

test_that("MgDb-class select return",{
    expect_equal(mgDb_select(testMgDb, type = c("seq","tree")),
                 list(seq = test_seq, tree = testMgDb@tree))

    expect_equal(mgDb_select(testMgDb, type = c("taxa","tree")),
                 list(taxa = test_taxa_df, tree = testMgDb@tree))

    expect_equal(mgDb_select(testMgDb, type = c("seq","tree")),
                 list(seq = test_seq, tree = testMgDb@tree))

    expect_equal(mgDb_select(testMgDb, type = "all"),
                 list(taxa = test_taxa_df,
                      seq = test_seq,
                      tree = testMgDb@tree))
})

## TODO add tests for Greengenes format


test_that("MgDb-class select taxa",{
    test_select_taxa <- mgDb_select(
        testMgDb,type = "taxa",
        keys = c("tax_51", "tax_53"),
        keytype = "Genus")

    ## test type
    expect_is(test_select_taxa,"tbl_df")

    ## test value
    expect_equal(test_select_taxa, taxa[c(2,4),])
})


test_that("MgDb-class select seq", {
    test_select_seq <- mgDb_select(
        testMgDb,type = "seq",
        keys = c("tax_51", "tax_53"),
        keytype = "Genus")

    ## test type
    expect_is(test_select_seq, "DNAStringSet")

    ## test value
    ## Using test equivalent instead of test equal due to attribute differences
    expect_equivalent( test_select_seq, test_seq[c(2,4)])
})



test_that("MgDb-class select tree", {
    test_select_tree <- mgDb_select(
        testMgDb,type = "tree",
        keys = c("tax_51", "tax_53"),
        keytype = "Genus")

    ## test type
    expect_is(test_select_tree, "phylo")

    ## test value
    expect_equal(test_select_tree,
                 drop.tip(test_tree,
                          tip = test_tree$tip.label[-c(2,4)]))
})



test_that("MgDb-class select all",{
    test_select_all <- mgDb_select(
        testMgDb,type = "all",
        keys = c("tax_51", "tax_53"),
        keytype = "Genus")

    ## Test type
    expect_is(test_select_all, "list")
    expect_is(test_select_all$taxa, "tbl_df")
    expect_is(test_select_all$seq, "DNAStringSet")
    expect_is(test_select_all$tree, "phylo")

    ## test value taxa
    test_select_taxa <- mgDb_select(
        testMgDb,type = "taxa",
        keys = c("tax_51", "tax_53"),
        keytype = "Genus")

    expect_equal(test_select_all$taxa, test_select_taxa)

    ## test value seq
    test_select_seq <- mgDb_select(
        testMgDb,type = "seq",
        keys = c("tax_51", "tax_53"),
        keytype = "Genus")

    expect_equal(test_select_all$seq, test_select_seq)

    ## test value tree
    test_select_tree <- mgDb_select(
        testMgDb,type = "tree",
        keys = c("tax_51", "tax_53"),
        keytype = "Genus")

    expect_equal(test_select_all$tree, test_select_tree)

    ## Equal number of entries
    expect_equal(length(test_select_all$seq), nrow(test_select_all$taxa))
    expect_equal(nrow(test_select_all$taxa), ape::Ntip(test_select_all$tree))

})

## Using Entero GG85 as bug first identified when developing
## database-explore.Rmd vignette
test_that("MgDb-class select equal entries",{
    test_select_entero <- mgDb_select(get_gg13.8_85MgDb(),
                                      type = "all",
                                      keys = "Enterobacteriaceae",
                                      keytype = "Family")
    ## Equal number of entries
    expect_equal(length(test_select_entero$seq), nrow(test_select_entero$taxa))
    expect_equal(nrow(test_select_entero$taxa), ape::Ntip(test_select_entero$tree))
})