integration test 1

Integration test added for main function

.gitignore

@@ -14,4 +14,6 @@ sftp-config.json
 tests/testthat/Rplots.pdf
 *.pptx
 
-/tests/quantify_edits/
+/tests/quantify_edits/
+
+/tests/testthat/integration_test_1/

R/quantify_edits.R

@@ -72,6 +72,7 @@ quantify_edits <- function(
     spec_info_combo_overview_table = df_annotations,
     abundance_cutoff = run_params$abundance_cutoff)
 
+
   bam_files <- list_bam_files(base_directory = run_params$base_directory)
 
   logr::log_print(bam_files)

README.md

@@ -17,4 +17,3 @@ devtools::install_github('agmcfarland/BEiGUIDE')
 
 # Usage
 
-

tests/testthat/test-bam_file_to_table.R

@@ -1,13 +1,14 @@
 test_that("bam_file_to_table works", {
 
+  subsetted_test_data_path <- testthat::test_path('testdata', 'integration_1')
 
-  bam_file_path <- testthat::test_path('testdata', 'process_data', 'align', 'GTSP5614-neg-3.bin2.bam')
+  bam_file_path <- file.path(subsetted_test_data_path, 'process_data', 'align', 'GTSP5610-neg-1.bin1.bam')
 
   file.exists(bam_file_path)
 
   df_bam <- bam_file_to_table(bam_file_path)
 
-  testthat::expect_equal(nrow(df_bam), 172)
+  testthat::expect_equal(nrow(df_bam), 398787)
 
   testthat::expect_equal(ncol(df_bam), 9)
 

tests/testthat/test-list_bam_files.R

@@ -1,9 +1,9 @@
 testthat::test_that("list_bam_files works", {
 
-  bam_list <- list_bam_files(base_directory = testthat::test_path('testdata'))
+  subsetted_test_data_path <- testthat::test_path('testdata', 'integration_1')
 
-  testthat::expect_equal(length(bam_list), 1)
+  bam_list <- list_bam_files(base_directory = subsetted_test_data_path)
 
-  testthat::expect_equal(bam_list[1], testthat::test_path('testdata', 'process_data', 'align', 'GTSP5614-neg-3.bin2.bam'))
+  testthat::expect_equal(length(bam_list), 6)
 
 })

tests/testthat/test-make_edit_site_table.R

@@ -1,15 +1,17 @@
 test_that("make_edit_site_table works", {
 
-  df_ft_data <- pull_ft_data_tables(base_directory = testthat::test_path('testdata'))
+  subsetted_test_data_path <- testthat::test_path('testdata', 'integration_1')
 
-  df_annotations <- pull_combo_overview_table(base_directory = testthat::test_path('testdata'))
+  df_ft_data <- pull_ft_data_tables(base_directory = subsetted_test_data_path)
+
+  df_annotations <- pull_combo_overview_table(base_directory = subsetted_test_data_path)
 
   df_edit_sites <- make_edit_site_table(
     ft_data_table = df_ft_data,
     spec_info_combo_overview_table = df_annotations,
     abundance_cutoff = 3)
 
-  testthat::expect_equal(53, nrow(df_edit_sites))
+  testthat::expect_equal(11, nrow(df_edit_sites))
 
   testthat::expect_equal(13, ncol(df_edit_sites))
 

tests/testthat/test-parallel_bam_file_to_table.R

@@ -1,13 +1,14 @@
 test_that("parallel_bam_file_list_to_table works", {
 
+  subsetted_test_data_path <- testthat::test_path('testdata', 'integration_1')
 
-  bam_file_path <- testthat::test_path('testdata', 'process_data', 'align', 'GTSP5614-neg-3.bin2.bam')
+  bam_file_path <- file.path(subsetted_test_data_path, 'process_data', 'align', 'GTSP5610-neg-1.bin1.bam')
 
   file.exists(bam_file_path)
 
   df_bam <- parallel_bam_file_list_to_table(bam_file_path)
 
-  testthat::expect_equal(nrow(df_bam), 172)
+  testthat::expect_equal(nrow(df_bam), 398787)
 
   testthat::expect_equal(ncol(df_bam), 10)
 

tests/testthat/test-pull_combo_overview_table.R

@@ -1,7 +1,10 @@
 testthat::test_that("pull_combo_overview_table works", {
-  df_combo_overview <- pull_combo_overview_table(base_directory = testthat::test_path('testdata'))
 
-  testthat::expect_equal(15, nrow(df_combo_overview))
+  subsetted_test_data_path <- testthat::test_path('testdata', 'integration_1')
+
+  df_combo_overview <- pull_combo_overview_table(base_directory = subsetted_test_data_path)
+
+  testthat::expect_equal(2, nrow(df_combo_overview))
 
   testthat::expect_equal(7, ncol(df_combo_overview))
 

tests/testthat/test-pull_ft_data_tables.R

@@ -1,8 +1,10 @@
 testthat::test_that("pull_ft_data_tables works", {
 
-  df_ft_data <- pull_ft_data_tables(base_directory = testthat::test_path('testdata'))
+  subsetted_test_data_path <- testthat::test_path('testdata', 'integration_1')
 
-  testthat::expect_equal(14362, nrow(df_ft_data))
+  df_ft_data <- pull_ft_data_tables(base_directory = subsetted_test_data_path)
+
+  testthat::expect_equal(5815, nrow(df_ft_data))
 
   testthat::expect_equal(9, ncol(df_ft_data))
 

tests/testthat/test-quantify_edits.R

@@ -0,0 +1,27 @@
+test_that("quantify_edits works", {
+
+  test_data <- testthat::test_path('testdata', 'integration_1')
+
+  test_output <- file.path(testthat::test_path('integration_test_1'))
+
+  dir.create(test_output, showWarnings = FALSE)
+
+  quantify_edits(
+    base_directory = test_data,
+    output_directory = test_output,
+    n_processors = 8
+  )
+
+  df_edit_sites <- readRDS(file.path(test_output, 'quantify_edits', 'edit_sites.rds'))
+
+  df_base_percentages <- readRDS(file.path(test_output, 'quantify_edits', 'base_percentages.rds'))
+
+  testthat::expect_equal(nrow(df_edit_sites), 11)
+
+  testthat::expect_equal(ncol(df_edit_sites), 13)
+
+  testthat::expect_equal(nrow(df_base_percentages), 147)
+
+  testthat::expect_equal(ncol(df_base_percentages), 16)
+
+})