TODO List
TODO
This a Carlos/Germain Task-list. This might be very general brainstorming or specific points.
Make homogeneous names for intensities vs intensity in particular in Peak class and subclasses => easier transfert between classes-
isotopic_patter_attribution
cutt_off_factor works only with 13C1, it should be a factor linked to the defined isotopic_pattern, for exmple, if the isotopic patter is (5,10), the cut_off_factor should be related to 10B1 and not to 13C1.✅ -
Re-make kendrick_attribution.py usingFormulaGrid
and enhancing the algorithm.✅ -
UseFormulaGridNumpy
inassignment
andattribution
FormulaGirdNumpy.isotopic_information
produce a false information.✅ FormulaGridNumpy
-->FormulaGrid
-
Update Notebooks:Molecular_Formula_Assignment,Molecular_Formula_Kendricks,FeatureDetection,KmeansDetection,Recalibration.✅ -
Formula => move isotopic pattern fromComposition
toFormula
✅ : Another solution was given, now theIsotopic_Pattern
class works for both classesFormula
andComposition
. Terminate test on recalibration-
ROI some methods do not work because any more (noise cleaning, unifying ROIs)✅ -
Implement a genericread_file
to load any peaklist✅ function isread_peaklist
. - plot DBE using family group vs family ?
checkself.formulas
andself.molecular_formulas
andstr_formulas
=> duplicated attributes ?-
There is no test forisotopic_pattern_attribution
✅ - ~~ There is no test for
pyc2mc.io.caliblist.CalibList
~~✅ -
Peaklist
inherit fromMutableSequence
python class✅ PeakList
inherit fromSequence
. -
=> finally not necessaryCalibListBuilding
inherit fromMutableSequence
python class. -
=> SequenceCalibList
inherit fromlist
instead ofMutableSequence
in Formula, nominal_mass is the floor of ion exact massSeparate caliblist.py in two modules, one in io/ and another in core/ to split the class methods from the main object class CalibList.
Still not done
- Homogeneise a global Polarity class: either int either string
- Check unifying roi operation (for now is inhibited).
- Attribution may remove peaklist_properties, or peaklist_properties are not transferred. Need to transfer peak. The same in kendrick.
Edited by Salvato Vallverdu Germain