tests/testthat/test_reader.R

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

context("Read Immuno Seq")
library(LymphoSeq2)
library(tidyverse)

test_that("Reads a single AIRR file correctly", {
  stable <- LymphoSeq2::readImmunoSeq("test_data/015V12001549_CFAR.tsv", threads = 1)
  snuc <- base::length(base::unique(stable$junction))
  srow <- base::nrow(stable)
  tot_freq <- stable %>%
    dplyr::pull(duplicate_frequency) %>%
    base::sum()
  expect_equal(base::nrow(stable), 1000)
  expect_equal(snuc, srow)
  expect_equal(tot_freq, 1)
})

test_that("Reads a list of AIRR file correctly", {
  stable <- LymphoSeq2::readImmunoSeq(c("test_data/015V12001549_CFAR.tsv", "test_data/015V12001685_CFAR_R.tsv"),
    threads = 1
  )
  srow <- base::nrow(stable)
  ctable <- tibble::tibble(
    repertoire_id = c("015V12001549_CFAR", "015V12001685_CFAR_R"),
    tot_freq = c(1, 1),
    nrows = c(1000, 1000),
    nnuc = c(1000, 1000)
  ) %>%
    dplyr::mutate(
      nrows = base::as.integer(nrows),
      nnuc = base::as.integer(nnuc)
    )
  stable <- stable %>%
    dplyr::group_by(repertoire_id) %>%
    dplyr::summarize(
      tot_freq = base::sum(duplicate_frequency),
      nrows = dplyr::n(),
      nnuc = base::length(base::unique(junction))
    )
  expect_equal(srow, 2000)
  expect_true(dplyr::all_equal(ctable, stable))
})

test_that("Reads AIRR files from a path correctly", {
  stable <- LymphoSeq2::readImmunoSeq("test_data/", threads = 1)
  srow <- base::nrow(stable)
  ctable <- tibble::tibble(
    repertoire_id = c("015V12001549_CFAR", "015V12001685_CFAR_R", "015V12003105_CFAR", "015V06013979_CFAR"),
    tot_freq = c(1, 1, 1, 1),
    nrows = c(1000, 1000, 1000, 1000),
    nnuc = c(1000, 1000, 1000, 1000)
  ) %>%
    dplyr::mutate(
      nrows = base::as.integer(nrows),
      nnuc = base::as.integer(nnuc)
    )
  stable <- stable %>%
    dplyr::group_by(repertoire_id) %>%
    dplyr::summarize(
      tot_freq = base::sum(duplicate_frequency),
      nrows = dplyr::n(),
      nnuc = base::length(base::unique(junction))
    )
  expect_equal(srow, 4000)
  expect_true(dplyr::all_equal(ctable, stable))
})

test_that("Creates correct columns", {
  stable <- LymphoSeq2::readImmunoSeq("test_data/015V12001549_CFAR.tsv", threads = 1)
  scol <- base::ncol(stable)
  sfields <- colnames(stable)

  airr_headers_path <- system.file("extdata", "AIRR_fields.csv", package = "LymphoSeq2")
  airr_table <- readr::read_csv(airr_headers_path, trim_ws = TRUE)
  airr_fields <- colnames(airr_table)
  expect_equal(scol, 145)
  expect_equal(sfields, c(airr_fields, "bio_identity"))
})