start readMSP testing

ipb-halle · Mar 5, 2024 · 595c0c3 · 595c0c3
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diff --git a/inst/extdata/testdata/readMSPreturnObj.Rdata b/inst/extdata/testdata/readMSPreturnObj.Rdata
diff --git a/tests/testthat/test_fileinput.R b/tests/testthat/test_fileinput.R
@@ -28,3 +28,70 @@ test_that("MS-Dial 4.X", {
 #     expect_equal(ncol(data$dataFrame), 41)
 })
 
+test_that("MSP reading works", {
+
+  if(FALSE) {
+  fileSpectra <- system.file("extdata/showcase/Metabolite_profile_showcase.msp", package = "MetFamily")
+  #load(system.file("extdata/testdata/readMSPreturnObj.Rdata", package = "MetFamily"))
+
+  returnObj <- parseMSP(fileSpectra = fileSpectra, 
+                        minimumIntensityOfMaximalMS2peak = 2000, 
+                        minimumProportionOfMS2peaks = 0.05, 
+                        neutralLossesPrecursorToFragments = TRUE,
+                        neutralLossesFragmentsToFragments = FALSE,
+                        progress = FALSE)
+
+
+  expect_equal(returnObj$numberOfSpectra, 2640)
+  expect_equal(returnObj$numberOfSpectraOriginal, 5824)
+  expect_equal(returnObj$numberOfMS2PeaksOriginal, 145973)
+  expect_equal(returnObj$numberOfMS2PeaksWithNeutralLosses, 68738)
+  expect_equal(returnObj$numberOfMS2PeaksAboveThreshold, 34369)
+  expect_equal(returnObj$numberOfMS2PeaksBelowThreshold, 109797)
+  expect_equal(returnObj$numberOfTooHeavyFragments, 1807)
+  expect_equal(returnObj$numberOfSpectraDiscardedDueToNoPeaks, 15)
+  expect_equal(returnObj$numberOfSpectraDiscardedDueToMaxIntensity, 3163)
+  expect_equal(returnObj$numberOfSpectraDiscardedDueToTooHeavy, 5)
+  expect_equal(length(returnObj$precursorMz), 2640)
+  expect_equal(returnObj$precursorMz[1], 85)
+  expect_equal(length(returnObj$precursorRt), 2640)
+  expect_equal(returnObj$precursorRt[1], 10.98)
+
+  }
+
+  # > str(returnObj, max.level = 1)
+  # List of 14
+  # $ fileSpectra                              : chr "/tmp/RtmpL82I4E/ff16bb92ac5e87cb202eec2e/0.msp"
+  # $ spectraList                              :List of 2640
+  # $ numberOfSpectra                          : int 2640
+  # $ numberOfSpectraOriginal                  : int 5824
+  # $ numberOfMS2PeaksOriginal                 : num 145973
+  # $ numberOfMS2PeaksWithNeutralLosses        : num 68738
+  # $ numberOfMS2PeaksAboveThreshold           : num 34369
+  # $ numberOfMS2PeaksBelowThreshold           : num 109797
+  # $ numberOfTooHeavyFragments                : num 1807
+  # $ numberOfSpectraDiscardedDueToNoPeaks     : num 15
+  # $ numberOfSpectraDiscardedDueToMaxIntensity: num 3163
+  # $ numberOfSpectraDiscardedDueToTooHeavy    : num 5
+  # $ precursorMz                              : num [1:2640] 85 85 85 85 85 ...
+  # $ precursorRt                              : num [1:2640] 10.98 7.42 12.4 16.26 13 ...
+  # 
+
+
+
+  ##
+  ## returnObj contains the following elements:
+  ##
+
+  # returnObj <- list()
+  # returnObj$fileSpectra <- fileSpectra
+  # returnObj$spectraList <- list()
+  # returnObj$numberOfSpectra <- 0
+  # returnObj$numberOfMS2PeaksOriginal <- 0
+  # returnObj$numberOfMS2PeaksWithNeutralLosses <- 0
+  # returnObj$numberOfMS2PeaksAboveThreshold <- 0
+  # returnObj$numberOfMS2PeaksBelowThreshold <- 0
+  # returnObj$precursorMz <- vector(mode = "numeric")
+  # returnObj$precursorRt <- vector(mode = "numeric")
+
+})