tests/testthat/test_countkmer.R

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

context("Count k-mers in nucleotide sequence")
library(LymphoSeq2)
library(tidyverse)

test_that("Number of k-mers are counted correctly", {
  junction <- "ATCGATCAC"
  study_table <- LymphoSeq2::readImmunoSeq("test_data/015V06013979_CFAR.tsv", threads = 1)
  ktable <- LymphoSeq2::countKmer(study_table = study_table, k = 3)
  num_rows <- base::nrow(ktable)
  rep_id <- study_table |>
    dplyr::pull(repertoire_id) |>
    unique()
  Kmer <- c(
    "AAA", "AAC", "AAG", "AAT", "ACA", "ACC", "ACG", "ACT", "AGA",
    "AGC", "AGG", "AGT", "ATA", "ATC", "ATG", "ATT", "CAA", "CAC",
    "CAG", "CAT", "CCA", "CCC", "CCG", "CCT", "CGA", "CGC", "CGG",
    "CGT", "CTA", "CTC", "CTG", "CTT", "GAA", "GAC", "GAG", "GAT",
    "GCA", "GCC", "GCG", "GCT", "GGA", "GGC", "GGG", "GGT", "GTA",
    "GTC", "GTG", "GTT", "TAA", "TAC", "TAG", "TAT", "TCA", "TCC",
    "TCG", "TCT", "TGA", "TGC", "TGG", "TGT", "TTA", "TTC", "TTG",
    "TTT"
  )
  Count <- c(
    558, 761, 762, 328, 1750, 1090, 503, 1626, 1300, 3260, 1186,
    1316, 362, 1207, 457, 592, 755, 1078, 4335, 794, 2623, 1890,
    796, 1402, 529, 612, 1734, 231, 868, 1986, 2630, 1957, 1036,
    1802, 1514, 489, 2034, 2685, 691, 1877, 2030, 1784, 3380, 661,
    1289, 441, 1848, 665, 194, 1275, 424, 1018, 694, 1037, 1379,
    2411, 902, 1566, 1534, 2006, 390, 1816, 1044, 1806
  )
  kmer_table <- tibble::tibble(Kmer, Count)
  kmer_table <- magrittr::set_colnames(kmer_table, c("Kmer", rep_id))
                
  expect_equal(num_rows, 64)
  expect_equal(ktable, kmer_table)
})