set.seed(42) tempy <- tempdir() dir.create(file.path(tempy, "idbac_tests")) sql_dir <- file.path(tempy, "idbac_tests", "sqlite") dir.create(sql_dir) protein_masses <- list(26978, c(5112, 6625), c(5873, 6261, 6584, 6908, 7108, 7512, 7877, 7982, 8538, 8609, 14085, 16087, 19514, 23704, 24162, 24295, 24978, 27095, 28946, 29040), c(3091, 3951, 4070, 4772, 4821, 4846, 5090, 6488, 6493, 6675, 6962, 7187, 7252, 7655, 7672, 8034, 8913, 9030, 9469, 10030, 10071, 10514, 10573, 10599, 10867, 10958, 11165, 11476, 11705, 11910, 11948, 12413, 12984, 13178, 13245, 13368, 13455, 14019, 14081, 14272, 14322, 14467, 14730, 14812, 15034, 15270, 15490, 15615, 16078, 16205, 16247, 16298, 16814, 17062, 17668, 17790, 17974, 18325, 18326, 18984, 19176, 19621, 19691, 20310, 20443, 20717, 20808, 20869, 21127, 21412, 22320, 22540, 22718, 23004, 23017, 23943, 24387, 24459, 24732, 24869, 25352, 25387, 25742, 26525, 26926, 27005, 27059, 27529, 28133, 28342, 28657, 28735, 28854, 28913, 29333, 29342, 29368, 29374, 29418, 29484)) intensities <- lapply(protein_masses, function(x) rep(100, length(x))) protein_spectra <- createFuzzyVector(massStart = 2000, massEnd = 30000, ppm = 8000, massList = protein_masses, intensityList = intensities) small_masses <- list(1208, c(1214, 2614), c(225, 419, 461, 531, 546, 679, 822, 1076, 1484, 1709, 1775, 1890, 1893, 2138, 2259, 2414, 2442, 2624, 2724, 2971), c(244, 297, 302, 308, 315, 334, 343, 346, 389, 401, 427, 468, 551, 565, 610, 675, 696, 728, 738, 760, 791, 840, 841, 906, 961, 962, 987, 989, 990, 998, 1018, 1033, 1049, 1060, 1123, 1154, 1156, 1165, 1210, 1240, 1243, 1280, 1297, 1298, 1299, 1311, 1455, 1487, 1513, 1518, 1537, 1543, 1587, 1592, 1623, 1636, 1659, 1701, 1720, 1737, 1783, 1820, 1821, 1825, 1860, 1899, 1978, 2011, 2080, 2114, 2134, 2137, 2189, 2212, 2265, 2325, 2339, 2345, 2389, 2394, 2417, 2436, 2441, 2466, 2502, 2509, 2552, 2567, 2617, 2667, 2731, 2745, 2754, 2796, 2827, 2833, 2887, 2929, 2934, 2978)) intensities <- lapply(small_masses, function(x) rep(100, length(x))) smallmol_spectra <- createFuzzyVector(massStart = 200, massEnd = 3000, ppm = 100, massList = small_masses, intensityList = intensities) smallmol_spectra <- lapply(1:ncol(smallmol_spectra), function(x){ MALDIquant::createMassSpectrum(mass = as.numeric(rownames(smallmol_spectra)), intensity = smallmol_spectra[, x]) }) protein_spectra <- lapply(1:ncol(protein_spectra), function(x){ MALDIquant::createMassSpectrum(mass = as.numeric(rownames(protein_spectra)), intensity = protein_spectra[, x]) }) suppressWarnings({ names(protein_spectra) <- LETTERS[1:4] names(smallmol_spectra) <- LETTERS[1:4] spectra <- c(smallmol_spectra, protein_spectra) spectra <- split(spectra, names(spectra)) }) test_that("created expected demo spectra", { expect_true(all(sapply(protein_spectra, function(x) inherits(x, "MassSpectrum")))) expect_true(all(lengths(lapply(protein_spectra, function(x) x@mass)) == 1771)) expect_true(all(lengths(lapply(protein_spectra, function(x) x@intensity)) == 1771)) expect_true(all(sapply(smallmol_spectra, function(x) inherits(x, "MassSpectrum")))) expect_true(all(lengths(lapply(smallmol_spectra, function(x) x@mass)) == 140021)) expect_true(all(lengths(lapply(smallmol_spectra, function(x) x@intensity)) == 140021)) }) # Save as mzml ------------------------------------------------------------ mzml_path <- file.path(tempy, "idbac_tests", "mzml", fsep = "/") dir.create(mzml_path) mzml_path <- normalizePath(mzml_path, "/") for (i in seq_along(spectra)) { MALDIquantForeign::exportMzMl(unlist(spectra[[i]]), file.path(mzml_path, paste0(LETTERS[[i]], ".mzml")) ) } IDBacApp::idbac_create("sql_from_mzml", sql_dir) new_idbac_mzml <- IDBacApp::idbac_connect("sql_from_mzml", sql_dir)[[1]] test_that("IDBac sql from mzml", { expect_message( db_from_mzml(mzFilePaths = list.files(mzml_path, full.names = T), sampleIds = basename(tools::file_path_sans_ext(list.files(mzml_path, full.names = T))), idbacPool = new_idbac_mzml, acquisitionInfo = NULL, halfWindowSize = 2) ) }) # Create txt -------------------------------------------------------------- a <- tempdir() csv_path <- file.path(tempy, "idbac_tests", "csv", fsep = "/") dir.create(csv_path) csv_path <- normalizePath(csv_path, "/") dir.create(file.path(tempy, "idbac_tests", "csv", "small", fsep = "/")) dir.create(file.path(tempy, "idbac_tests", "csv", "protein", fsep = "/")) for (i in seq_along(smallmol_spectra)) { MALDIquantForeign::exportCsv(smallmol_spectra[[i]], file.path(csv_path, "small", paste0(names(smallmol_spectra)[[i]], ".csv")) ) } for (i in seq_along(protein_spectra)) { MALDIquantForeign::exportCsv(protein_spectra[[i]], file.path(csv_path, "protein", paste0(names(protein_spectra)[[i]], ".csv")) ) } p_files <- list.files(file.path(csv_path, "protein"), full.names = T) s_files <- list.files(file.path(csv_path, "small"), full.names = T) new_mzml <- file.path(csv_path, "mzml") dir.create(new_mzml) delim_tomzml_results <- IDBacApp::delim_to_mzml(proteinPaths = p_files, proteinNames = LETTERS[1:4], smallMolPaths = s_files, smallMolNames = LETTERS[1:4], exportDirectory = new_mzml, centroid = F) test_that("delim_to_mzml()", { expect_identical(length(delim_tomzml_results), 4L) expect_identical(names(delim_tomzml_results), LETTERS[1:4]) expect_true(all(sapply(delim_tomzml_results, file.exists))) expect_equal(unique(tools::file_ext(delim_tomzml_results)), "mzml") }) IDBacApp::idbac_create("sql_from_csv", sql_dir) new_idbac <- IDBacApp::idbac_connect("sql_from_csv", sql_dir)[[1]] test_that("IDBac sql from csv", { expect_message( IDBacApp::db_from_mzml(mzFilePaths = unname(delim_tomzml_results), sampleIds = names(delim_tomzml_results), idbacPool = new_idbac, acquisitionInfo = NULL, halfWindowSize = 2) ) }) samps <- idbac_available_samples(pool = new_idbac, type = "all") smallspec <- idbac_get_spectra(pool = new_idbac, sampleID = LETTERS[1:4], type = "small") protspec <- idbac_get_spectra(pool = new_idbac, sampleID = LETTERS[1:4], type = "protein") test_that("IDBac sql from csv is correct", { expect_identical(length(smallspec), 4L) expect_identical(length(protspec), 4L) expect_true(all(sapply(protspec, function(x) inherits(x, "MassSpectrum")))) expect_known_hash(smallspec, "78f3c87c6b") expect_known_hash(protspec, "802b0e3cf5") }) new_idbac_spectra <- DBI::dbGetQuery(new_idbac, "SELECT * FROM spectra") new_idbac_mzml_spectra <- DBI::dbGetQuery(new_idbac_mzml, "SELECT * FROM spectra") test_that("compare the two created db spectra table", { # Don't include xml hash because it includes file path expect_true(all(mapply(identical, new_idbac_spectra[4,-3], new_idbac_mzml_spectra[4,-3]))) })