tests/testthat/test_mdDb-annotateFeatures.R

In HCBravoLab/metagenomeFeatures: Exploration of marker-gene sequence taxonomic annotations

library(metagenomeFeatures)
library(dplyr)


context("Testing annotateFeatures")

OTU <- c(4,4,4,3,2)
Keys_not <- c(1,1,1,1,1)
Keys <- c(1,2,3,4,5)

incomplete_query_df <- data.frame(OTU)
wrong_query_df <- data.frame(Keys_not, OTU)
query_df <- data.frame(Keys, OTU)
query_vctr <- Keys


# check parameters

test_that("annotateFeatures parameter check", {
    expect_error(annotateFeatures(testMgDb))
    expect_error(annotateFeatures(testMgDb, query = NULL))
    expect_error(annotateFeatures(testMgDb, incomplete_query_df))
    expect_error(annotateFeatures(testMgDb, wrong_query_df))
})

test_that("mgFeatures query types", {
    expect_is(annotateFeatures(testMgDb, query_df), "mgFeatures")
    expect_is(annotateFeatures(testMgDb, query_vctr), "mgFeatures")
})

# check resulting mgFeatures object result
test_that("mgFeatures accessory", {
    features_obj <- annotateFeatures(testMgDb, query_df)

    # check type breakdown of mgFeatures object
    expect_is(features_obj@metadata, "list")
    expect_is(features_obj@refDbSeq, "DNAStringSet")
    expect_is(features_obj@refDbTree, "phylo")
    expect_is(features_obj@listData, "list")

    expect_is(mgF_seq(features_obj), "DNAStringSet")
    expect_is(mgF_taxa(features_obj), "DataFrame")
    expect_is(mgF_tree(features_obj), "phylo")
    expect_is(mgF_meta(features_obj), "list")
})