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Add assertion for lipid workflow annotataion results
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tests/test_wf_lipidomics.py

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -82,7 +82,7 @@ def test_lipidomics_workflow():
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ms1_params.mass_spectrum.noise_min_mz, ms1_params.mass_spectrum.min_picking_mz = 0, 0
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ms1_params.mass_spectrum.noise_max_mz, ms1_params.mass_spectrum.max_picking_mz = np.inf, np.inf
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ms1_params.ms_peak.legacy_resolving_power = False
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ms1_params.molecular_search.url_database = "postgresql://coremsdb:coremsmolform@postgres:5432/molformula"
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ms1_params.molecular_search.url_database = ""
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ms1_params.molecular_search.usedAtoms = {
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'C': (10, 30),
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'H': (18, 200),
@@ -192,6 +192,7 @@ def test_lipidomics_workflow():
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exporter.report_to_csv(molecular_metadata=lipid_metadata)
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report = exporter.to_report(molecular_metadata=lipid_metadata)
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assert report['Ion Formula'][1] == 'C24 H47 O2'
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assert report['Lipid Species'][1] == 'FA 24:0'
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# Import the hdf5 file, assert that its df is same as above and that we can plot a mass feature
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parser = ReadCoreMSHDFMassSpectra(

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