context("Testing SVM files")
test_that("Testing read functions", {
expect_error(tor_read_svm_data_file("DNE"), "svm file does not seem to exist")
# read a good test file
expect_true(is.data.frame(svm_data <- tor_read_svm_data_file(file.path("test_data", "svm_pred_results.csv"))))
expect_equal(nrow(svm_data), 101721)
# check for warnings in a bad test file
expect_error(
suppressWarnings(tor_read_svm_data_file(file.path("test_data", "svm_pred_results_bad.csv"))),
"missing column")
})
test_that("SVM processiong works", {
expect_error(tor_filter_peptides_by_spectral_fit_quality())
expect_error(tor_filter_peptides_by_spectral_fit_quality(5), "wrong data type")
})
test_that("Renaming proteins works", {
# make sure errors are thrown
expect_error(tor_recode_protein_ids())
expect_error(tor_recode_protein_ids(5), "wrong data type")
expect_error(tor_recode_protein_ids(data_frame(x=1)), "column .* does not exist")
expect_error(tor_recode_protein_ids(data_frame(prot_id=1), prot_col = "my_protein"), "column .* does not exist")
expect_error(tor_recode_protein_ids(data_frame(prot_id=1)), "mapping text file.* is required")
expect_error(tor_recode_protein_ids(data_frame(prot_id=1), renaming_protein_map_file = "DNE"))
expect_error(tor_recode_protein_ids(data_frame(prot_id = 1), file.path("test_data", "rename_prot_bad.xlsx")), "column .* does not exist")
# test specific data
my_test_data <- data_frame(prot_id = c("Q1PI83:KAD", "Q1PI83:KAD", "OTHER"))
expect_message(result <- tor_recode_protein_ids(my_test_data, file.path("test_data", "rename_prot.xlsx")), "2 protein .* 1 different")
expect_equal(result, data_frame(prot_id = c("KAD", "KAD", "OTHER")))
})
#tests for "tor_calculate_labeled_fraction" function
test_that("tor_calculate_labeled_fraction works", {
# - test that filtered_data file is correct format
expect_error(tor_calculate_labeled_fraction())
expect_error(tor_calculate_labeled_fraction(5), "wrong data type")
# test specific data
# test that correct inputs used to calculate
# test that fraculab and fraclab calculations are correct
})
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