tests/testthat/test-read_fasta.R

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

test_that("Read in fasta formatted data generates data frame", {
  temp <- tempfile()
  write(">seqA\nATGCATGC\n>seqB\nTACGTACG", file = temp)
  write(">seqC\nTCCGATGC", file = temp, append = TRUE)
  write(">seqC\n...T-C--CGATGC...", file = temp, append = TRUE)
  write(">seqD B.ceresus UW85\nTCCGATGC", file = temp, append = TRUE)
  write(">seq4\tE. coli K12\tBacteria;Proteobacteria;\nTCCGATGC",
    file = temp,
    append = TRUE
  )
  write(">seq_4\tSalmonella LT2\tBacteria;Proteobacteria;\nTCCGATGC",
    file = temp, append = TRUE
  )
  write(">seqE B.ceresus UW123\nTCCGATGC\nTCCGATGC",
    file = temp,
    append = TRUE
  )
  write(">seqD|B.cereus UW85\nTCCGATGC", file = temp, append = TRUE)
  write(">seqD.B.cereus UW85\nTCCGATGC", file = temp, append = TRUE)

  sequence_df <- read_fasta(temp)

  expected <- data.frame(
    id = c(
      "seqA", "seqB", "seqC", "seqC", "seqD", "seq4", "seq_4", "seqE",
      "seqD|B.cereus", "seqD.B.cereus"
    ),
    sequence = c(
      "ATGCATGC", "TACGTACG", "TCCGATGC", "TCCGATGC", "TCCGATGC", "TCCGATGC",
      "TCCGATGC", "TCCGATGCTCCGATGC", "TCCGATGC", "TCCGATGC"
    ),
    comment = c(
      "", "", "", "", "B.ceresus UW85",
      "E. coli K12\tBacteria;Proteobacteria;",
      "Salmonella LT2\tBacteria;Proteobacteria;", "B.ceresus UW123",
      "UW85", "UW85"
    )
  )

  expect_equal(sequence_df, expected)
  expect_equal(read_fasta(temp, degap = TRUE), expected)

  expected2 <- expected
  expected2$sequence[4] <- "...T-C--CGATGC..."

  expect_equal(read_fasta(temp, degap = FALSE), expected2)
})