tests/testthat/_test_file_io.r

In cmmr/rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
# Biom File Read/Write
#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

context("Biom File Read/Write")

biom <- readRDS("inputs/biom.rds")
biom$info$id <- "full biom"


#----------------------------------------------------------
# Edge cases
#----------------------------------------------------------

onesample <- biom
onesample[['counts']] <- onesample[['counts']][,1]
onesample$info$id <- "onesample"
onesample <- repair(onesample)

onetaxa <- biom
onetaxa[['counts']] <- onetaxa[['counts']][1,]
onetaxa$info$id <- "onetaxa"
onetaxa <- repair(onetaxa)


lapply(list(biom, onesample, onetaxa), function (x) {
  
  
  #----------------------------------------------------------
  # Write/Read Classic Tabular Format
  #----------------------------------------------------------
  
  test_that(paste("TSV Intermediate for", x$info$id), {
    
    fp <- tempfile(fileext = ".gz")
    write_biom(x, fp, format="tab")
    tsv <- read_biom(fp)
    unlink(fp)
    
    expect_equivalent(as.matrix(x$counts), as.matrix(tsv$counts))
    expect_equivalent(x$taxonomy,          tsv$taxonomy)
    expect_equivalent(x$shape,             tsv$shape)
  })
  
  
  #----------------------------------------------------------
  # Write/Read BIOM Format 1.0 (JSON)
  #----------------------------------------------------------
  
  test_that(paste("JSON Intermediate for", x$info$id), {
    
    fp <- tempfile(fileext = ".bz2")
    write_biom(x, fp, format="json")
    json <- read_biom(fp)
    unlink(fp)
    
    expect_equivalent(x$counts,    json$counts)
    expect_equivalent(x$phylogeny, json$phylogeny)
    expect_equivalent(x$metadata,  json$metadata)
    expect_equivalent(x$taxonomy,  json$taxonomy)
    expect_equivalent(x$shape,     json$shape)
  })
  
  
  #----------------------------------------------------------
  # Write/Read BIOM Format 2.1 (HDFS)
  #----------------------------------------------------------
  if (requireNamespace("rhdf5", quietly = TRUE)) {
    
    test_that(paste("HDF5 Intermediate for", x$info$id), {
      
      fp <- tempfile()
      write_biom(x, fp, format="hdf5")
      hdf5 <- read_biom(fp)
      unlink(fp)
      
      expect_equivalent(x$counts,    hdf5$counts)
      expect_equivalent(x$phylogeny, hdf5$phylogeny)
      expect_equivalent(x$metadata,  hdf5$metadata)
      expect_equivalent(x$taxonomy,  hdf5$taxonomy)
      expect_equivalent(x$shape,     hdf5$shape)
    })
    
  }
})


remove("biom", "onesample", "onetaxa")