Tests: OpenMS DDA (#549)

* fix: prioritized the use of subordinate metadata when choosing between feature level and subordinate level * tests: updated failing tests with new output * tests: remaking test data for DDA and updating tests * tests, examples: updated DDA tests and examples * tests: removed unneeded DDA test directories and files * tests: updates to utilities due to additional files * Updated contrib builds url and use of --user when installing python on MacOS Co-authored-by: bertrandboudaud <[email protected]>
AutoFlowResearch · Sep 12, 2022 · ef0093c · ef0093c
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -113,7 +113,7 @@ jobs:
  brew install cppcheck gnuplot
  brew install libomp
  brew install eigen
- pip3 install -r tools/smartpeak/requirements.txt
+ pip3 install -r tools/smartpeak/requirements.txt --user
  - run:
  name: "Pull latest (only release)"
  command: |
@@ -130,7 +130,7 @@ jobs:
  git clone --branch develop --depth 1 https://github.com/OpenMS/OpenMS.git &&
  cd OpenMS
  mkdir contrib_build && cd contrib_build
- curl -C - -O https://abibuilder.informatik.uni-tuebingen.de/archive/openms/contrib/macOS/10.15.4/x64/appleclang-11.0.0/contrib_build.tar.gz
+ curl -C - -O https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/macOS/10.15.4/x64/appleclang-11.0.0/contrib_build.tar.gz
  tar -xzf contrib_build.tar.gz
  sed -i '' 's/std::auto_ptr/std::unique_ptr/g' include/seqan/basic/test_system.h
  rm lib/libz.* && rm -rf lib/pkgconfig
@@ -254,7 +254,7 @@ jobs:
  }
  cd ~/OpenMS
  mkdir contrib_build; cd contrib_build
- $url_contrib = 'https://abibuilder.informatik.uni-tuebingen.de/archive/openms/contrib/windows/x64/msvc-14.2/contrib_build.tar.gz'
+ $url_contrib = 'https://abibuilder.cs.uni-tuebingen.de/archive/openms/contrib/windows/x64/msvc-14.2/contrib_build.tar.gz'
  $contrib_tmp = New-TemporaryFile | Rename-Item -NewName { $_ -replace 'contrib_tmp$', 'tar.gz' } –PassThru
  Invoke-WebRequest $url_contrib -OutFile $contrib_tmp
  7z x $contrib_tmp -o'.'

diff --git a/...a/DDA/features/Germicidin A standard 5e-2_GA1_01_27401_13_BatchName_1900-01-01_000000.csv b/...a/DDA/features/Germicidin A standard 5e-2_GA1_01_27401_13_BatchName_1900-01-01_000000.csv
@@ -1,11 +1,3 @@
 PrecursorMz ProductMz PrecursorCharge ProductCharge LibraryIntensity NormalizedRetentionTime PeptideSequence ModifiedPeptideSequence PeptideGroupLabel LabelType CompoundName SumFormula SMILES Adducts ProteinId UniprotId GeneName FragmentType FragmentSeriesNumber Annotation CollisionEnergy PrecursorIonMobility TransitionGroupId TransitionId Decoy DetectingTransition IdentifyingTransition QuantifyingTransition Peptidoforms
-195.101983934443155 111.045648931738441 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_111.046_HMDB:HMDB0000001 0 1 0 1 
-195.101983934443155 121.029828856042727 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_121.03_HMDB:HMDB0000001 0 1 0 1 
-195.101983934443155 122.033189965837721 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_122.033_HMDB:HMDB0000001 0 1 0 1 
-195.101983934443155 128.021266411122014 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_128.021_HMDB:HMDB0000001 0 1 0 1 
-195.101983934443155 148.933888727541955 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_148.934_HMDB:HMDB0000001 0 1 0 1 
-195.101983934443155 149.024935583932148 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_149.025_HMDB:HMDB0000001 0 1 0 1 
-195.101983934443155 150.028105165565989 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_150.028_HMDB:HMDB0000001 0 1 0 1 
-195.101983934443155 151.030013418740566 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_151.03_HMDB:HMDB0000001 0 1 0 1 
-195.101983934443155 167.03554334350784 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_167.036_HMDB:HMDB0000001 0 1 0 1 
-195.101983934443155 93.034766500219604 0 NA 9.078002343750001e04 -1.0 NA NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 scan=463_93.0348_HMDB:HMDB0000001 0 1 0 1 
+235.07477407390158 134.95685060594775 0 NA 476.0 329.319578751179961 NA HMDB:HMDB0000001 NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 HMDB:HMDB0000001_scan=440_134.957_370.346 0 1 0 1 
+235.07477407390158 217.105081882742866 0 NA 464.0 329.319578751179961 NA HMDB:HMDB0000001 NA -1 NA -1.0 -1.0 HMDB:HMDB0000001 HMDB:HMDB0000001_scan=440_217.105_370.346 0 1 0 1 
diff --git a/...eatures/Germicidin A standard 5e-2_GA1_01_27401_13_BatchName_1900-01-01_000000.featureXML b/...eatures/Germicidin A standard 5e-2_GA1_01_27401_13_BatchName_1900-01-01_000000.featureXML
diff --git a/...a/DDA/features/Germicidin A standard 5e-2_GA1_01_27401_13_BatchName_1900-01-01_000000.msp b/...a/DDA/features/Germicidin A standard 5e-2_GA1_01_27401_13_BatchName_1900-01-01_000000.msp
@@ -1,8 +1,7 @@
 Name: HMDB:HMDB0000001
-Retention Time: 390.259
-base peak intensity: 1.38524e05
-total ion current: 2.10504e05
-Num Peaks: 7
-93.0348:7280 111.046:2760 121.03:41376 122.033:3364 128.021:460 
-148.934:548 149.025:138524 
+Retention Time: 370.346
+base peak intensity: 476.0
+total ion current: 940.0
+Num Peaks: 2
+134.957:476 217.105:464 
 
diff --git a/src/examples/data/DDA/parameters.csv b/src/examples/data/DDA/parameters.csv
@@ -10,6 +10,8 @@ TargetedSpectraExtractor,AccurateMassSearchEngine:db:struct,['CHEMISTRY/HMDB2Str
 TargetedSpectraExtractor,AccurateMassSearchEngine:positive_adducts,CHEMISTRY/PositiveAdducts.tsv,TRUE,string,,This file contains the list of potential positive adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/PositiveAdducts.tsv in OpenMS/share is used.,
 TargetedSpectraExtractor,AccurateMassSearchEngine:negative_adducts,CHEMISTRY/NegativeAdducts.tsv,TRUE,string,,This file contains the list of potential negative adducts that will be looked for in the database. Edit the list if you wish to exclude/include adducts. By default CHEMISTRY/NegativeAdducts.tsv in OpenMS/share is used.,
 TargetedSpectraExtractor,relative_allowable_product_mass,50,TRUE,float,,Threshold m/z of a product relatively to the precurosor m/z (can be negative),
-TargetedSpectraExtractor,AccurateMassSearchEngine:ionization_mode,negative,TRUE,string,,"Positive or negative ionization mode? If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error.",
+TargetedSpectraExtractor,AccurateMassSearchEngine:ionization_mode,auto,TRUE,string,,"Positive or negative ionization mode? If 'auto' is used, the first feature of the input map must contain the meta-value 'scan_polarity'. If its missing, the tool will exit with error.",
 TargetedSpectraExtractor,AccurateMassSearchEngine:mass_error_value,10,TRUE,float,,Tolerance allowed for accurate mass search.,
-TargetedSpectraExtractor,AccurateMassSearchEngine:keep_unidentified_masses,TRUE,TRUE,bool,,Keep features that did not yield any DB hit.,
+TargetedSpectraExtractor,rt_window,60,TRUE,float,,,
+TargetedSpectraExtractor,mz_tolerance,0.001,TRUE,float,,,
+TargetedSpectraExtractor,AccurateMassSearchEngine:keep_unidentified_masses,TRUE,TRUE,bool,,,
diff --git a/...tpeak/data/DDA/Germicidin A standard.mzML → ...tests/class_tests/smartpeak/data/DDA.mzML b/...tpeak/data/DDA/Germicidin A standard.mzML → ...tests/class_tests/smartpeak/data/DDA.mzML