tests/testthat/test-assignSeqTaxonomy.R

In ananata/fastq2otu: FASTQ2OTU: Automate microbiome analyses

# R version 4.0.2 (2020-06-22)
# DADA2 version: 1.16.0

library(testthat)
library(dada2) # Install using BiocManager --- installed latticeExtra to v3.5.3 using devtools::install_version("latticeExtra", version = "0.6-28")

context("Assigning Taxonomy")

root <- #TODO 
setwd(root)

# Source files
source(paste0(root, "R/readConfig.R"))
source(paste0(root, "R/assignSeqTaxonomy.R"))
source(paste0(root, "R/setup.R"))

# Provide path to config file (update involved parameters in file)
config <- paste0(root, "inst/example-config.yml")
options <- yaml::yaml.load_file(config)
typeof(options$assignTaxLevels)


# Custruct sequence table (uses DADA2's built in dataset)
derep1 <- derepFastq(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
derep2 <- derepFastq(system.file("extdata", "sam2F.fastq.gz", package="dada2"))

dada1 <- dada(derep1, tperr1)
dada2 <- dada(derep2, tperr1)
test.seqtab <- dada2::makeSequenceTable(list(sample1=dada1, sample2=dada2))

# Perform Tests
test_that("Create fastAssignTaxa object using config file", {
  object <- readConfig(config, type = "assignTax")
  expect_true(!is.null(object))
})

test_that("Assign taxonomy using custom database", {
  otuTab <- assignSeqTaxonomy(seqtab = test.seqtab, object = readConfig(config, type = "assignTax"))
  expect_true(!is.null(otuTab))
})