Format ====== Several classes and functions to deal with common mass spectrometric format (mostly dealing with File I/O). :mod:`Transformation Collection` Module ------------------- TransformationCollection ^^^^^^^^^^^^^^ .. autoclass:: msproteomicstoolslib.format.TransformationCollection.TransformationCollection :members: :undoc-members: :show-inheritance: LightTransformationData ^^^^^^^^^^^^^^ .. autoclass:: msproteomicstoolslib.format.TransformationCollection.LightTransformationData :members: :undoc-members: :show-inheritance: :mod:`File Reader` Module ------------------- SWATHScoringReader ^^^^^^^^^^^^^^^^^ .. autoclass:: msproteomicstoolslib.format.SWATHScoringReader.ReadFilter :members: :undoc-members: :show-inheritance: .. autoclass:: msproteomicstoolslib.format.SWATHScoringReader.SWATHScoringReader :members: :undoc-members: :show-inheritance: .. autoclass:: msproteomicstoolslib.format.SWATHScoringReader.OpenSWATH_SWATHScoringReader :members: :undoc-members: :show-inheritance: .. autoclass:: msproteomicstoolslib.format.SWATHScoringReader.mProphet_SWATHScoringReader :members: :undoc-members: :show-inheritance: .. autoclass:: msproteomicstoolslib.format.SWATHScoringReader.Peakview_SWATHScoringReader :members: :undoc-members: :show-inheritance: .. autofunction:: msproteomicstoolslib.format.SWATHScoringReader.inferMapping :mod:`Data Matrix` Module ------------------- Functions for handling the output data matrix MatrixWriters ^^^^^^^^^^^^^^ .. autofunction:: msproteomicstoolslib.format.MatrixWriters.getwriter .. autoclass:: msproteomicstoolslib.format.MatrixWriters.IWriter :members: :undoc-members: :show-inheritance: .. autoclass:: msproteomicstoolslib.format.MatrixWriters.CsvWriter :members: :undoc-members: :show-inheritance: .. autoclass:: msproteomicstoolslib.format.MatrixWriters.XlsWriter :members: :undoc-members: :show-inheritance: .. autoclass:: msproteomicstoolslib.format.MatrixWriters.XlsxWriter :members: :undoc-members: :show-inheritance: :mod:`Spectral library` Module ------------------- Functions for handling SpectraST spectral library format Spectral library handler ^^^^^^^^^^^^^^^ .. autoclass:: msproteomicstoolslib.format.speclib_db_lib.Library :members: :undoc-members: :show-inheritance: .. autoclass:: msproteomicstoolslib.format.speclib_db_lib.SequenceHandler :members: :undoc-members: :show-inheritance: .. autoclass:: msproteomicstoolslib.format.speclib_db_lib.Spectra :members: :undoc-members: :show-inheritance: