tests/testthat/test-source.R

In grailbio/conta: Detect cross-contamination

# Copyright 2018 GRAIL, Inc. All rights reserved.
# Use of this source code is governed by the Apache 2.0
# license that can be found in the LICENSE file.

context("test source detect")

test_that("conta source detection run",  {

  expect_true(file.exists(in_dir_source))
  source_tsvs <- list.files(path = in_dir_source,
                            pattern = "*.nobaq.tsv", full.names = TRUE)
  dir.create(out_dir_source, recursive = TRUE)

  # Run conta on a set titration experiments with known source
  for (tsv_file in source_tsvs) {
    name <- basename(gsub(".subset.collapsed.nobaq.tsv", "", tsv_file))
    maf_tsv <- gsub("nobaq.tsv", "nobaq.maf.tsv", tsv_file)
    maf_tsv <- paste(out_dir_source, name, basename(maf_tsv), sep = "/")
    dir.create(dirname(maf_tsv), recursive = TRUE)
    conta::intersect_snps(tsv_file, maf_tsv, dbSNP_file_art, FALSE)
    conta_main(tsv_file = maf_tsv, sample_id = name, cores = 8,
               save_dir = dirname(maf_tsv), min_cf = 0.0004,
               outlier_frac = 0.001, lr_th = 0.05, blackswan = 0.2)
  }

  # Run conta source
  conta_source(base = out_dir_source, out_file = out_source,
               outlier_frac = 0, cores = 4, blackswan = 0.2)

  expect_true(file.exists(out_source))
  result <- read_data_table(out_source)
  expect_true(nrow(result) == 6)
  expect_false(result[6, source_call])
  expect_true(sum(result[2:5, source_call]) >= 3)
  expect_equal(sum(result[2:5, best_sample] == "170410_cfdna_100T_34795B_1"), 4)

  # Check if source files exist
  for (tsv_file in source_tsvs) {

    name <- basename(gsub(".subset.collapsed.nobaq.tsv", "", tsv_file))
    sfile <- paste(dirname(out_source), "/", name, ".gt.loh.source.tsv",
                   sep = "")
    expect_true(file.exists(sfile))
    sresult <- read_data_table(sfile)
    sind <- which(result$name == name)
    if (!is.na(result[sind]$best_sample)) {
      expect_true("source_lr1" %in% colnames(sresult))
      expect_true(!is.na(mean(sresult$source_lr1, na.rm = TRUE)))
    }
    if (!is.na(result[sind]$second_sample)) {
      expect_true("source_lr2" %in% colnames(sresult))
      expect_true(!is.na(mean(sresult$source_lr2, na.rm = TRUE)))
    }
    if (!is.na(result[sind]$third_sample)) {
      expect_true("source_lr3" %in% colnames(sresult))
      expect_true(!is.na(mean(sresult$source_lr3, na.rm = TRUE)))
    }
  }
  call_mt <- 0.005
  expect_true(result[2, best_gt_lr] > call_mt + result[2, avg_maf_lr])
  expect_true(result[3, best_gt_lr] > call_mt + result[3, avg_maf_lr])
  expect_true(result[4, best_gt_lr] > call_mt + result[4, avg_maf_lr])
  expect_true(result[5, best_gt_lr] > call_mt + result[5, avg_maf_lr])
})

test_that("conta source detection run single",  {

  expect_true(file.exists(in_dir_source_single))
  source_tsvs <- list.files(path = in_dir_source_single,
                            pattern = "*.nobaq.tsv", full.names = TRUE)
  dir.create(out_dir_source_single, recursive = TRUE)

  # Run conta on a set titration experiments with known source
  for (tsv_file in source_tsvs) {
    name <- basename(gsub(".subset.collapsed.nobaq.tsv", "", tsv_file))
    maf_tsv <- gsub("nobaq.tsv", "nobaq.maf.tsv", tsv_file)
    maf_tsv <- paste(out_dir_source_single, name, basename(maf_tsv), sep = "/")
    dir.create(dirname(maf_tsv), recursive = TRUE)
    conta::intersect_snps(tsv_file, maf_tsv, dbSNP_file_art, FALSE)
    conta_main(tsv_file = maf_tsv, sample_id = name, cores = 8,
               save_dir = dirname(maf_tsv), min_cf = 0.00005,
               outlier_frac = 0.001, lr_th = 0.05, blackswan = 0.2)
  }

  # Run conta source
  conta_source(base = out_dir_source_single, out_file = out_source_single,
               outlier_frac = 0.001, cores = 4, blackswan = 0.001)

  expect_true(file.exists(out_source_single))
  result <- read_data_table(out_source_single)
  expect_true(result[, .N] == 1)
  expect_false(result[1, source_call])
  expect_true(is.na(result[1, best_sample]))
  expect_true(is.na(result[1, best_gt_lr]))
})

test_that("conta source detection run double",  {

  expect_true(file.exists(in_dir_source_double))
  source_tsvs <- list.files(path = in_dir_source_double,
                            pattern = "*.nobaq.tsv", full.names = TRUE)
  dir.create(out_dir_source_double, recursive = TRUE)

  # Run conta on a set titration experiments with known source
  for (tsv_file in source_tsvs) {
    name <- basename(gsub(".subset.collapsed.nobaq.tsv", "", tsv_file))
    maf_tsv <- gsub("nobaq.tsv", "nobaq.maf.tsv", tsv_file)
    maf_tsv <- paste(out_dir_source_double, name, basename(maf_tsv), sep = "/")
    dir.create(dirname(maf_tsv), recursive = TRUE)
    conta::intersect_snps(tsv_file, maf_tsv, dbSNP_file_art, FALSE)
    conta_main(tsv_file = maf_tsv, sample_id = name, cores = 8,
               save_dir = dirname(maf_tsv), min_cf = 0.0001,
               outlier_frac = 0, lr_th = 0.02, blackswan = 0.2)
  }

  # Also add an empty conta result
  empty_out <- paste(out_dir_source_double, "sample1",
                     "sample1.conta.tsv", sep = "/")
  dir.create(dirname(empty_out))
  utils::write.table(empty_result("sample1"), file = empty_out, sep = "\t",
                     row.names = FALSE, quote = FALSE)

  # Run conta source
  conta_source(base = out_dir_source_double, out_file = out_source_double,
               outlier_frac = 0, cores = 1, blackswan = 0.02)

  expect_true(file.exists(out_source_double))
  result <- read_data_table(out_source_double)
  expect_true(nrow(result) == 2)
  expect_false(result[1, source_call])
  expect_true(result[2, source_call])
  expect_true(result[2, best_sample] == "170410_cfdna_100T_34795B_1")
  call_mt <- 0.005
  expect_true(result[1, best_gt_lr] < call_mt + result[1, avg_maf_lr])
  expect_true(result[2, best_gt_lr] > call_mt + result[2, avg_maf_lr])
})