|
|
| 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)) |
| |
| }) |
|
|
| |
|
|
| 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) |
| ) |
| }) |
|
|
|
|
|
|
|
|
| |
|
|
|
|
| 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", { |
| |
| expect_true(all(mapply(identical, new_idbac_spectra[4,-3], new_idbac_mzml_spectra[4,-3]))) |
| }) |
|
|
|
|
