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[CHANGE] ui option name for feature file boundaries #99

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merged 4 commits into from
Jan 24, 2024
+22 −17
Merged

[CHANGE] ui option name for feature file boundaries #99

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f863801
[CHANGE] ui option name for feature file boundaries
singjc Jan 23, 2024
c214b66
[RENAME] feature file peak pickign method
singjc Jan 24, 2024
989e919
FIX![GUI]: Feature File Peak Boundaries for raw GUI workflow
singjc Jan 24, 2024
ea57a56
Merge branch 'dev' of github.com:Roestlab/massseer into patch/ui_rena…
jcharkow Jan 24, 2024
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4 changes: 2 additions & 2 deletions massdash/server/ExtractedIonChromatogramAnalysisServer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,10 +127,10 @@ def main(self):
st.write(f"Loading XIC data... Elapsed time: {elapsed_time()}")

# Perform peak picking based on user settings
if peak_picking_settings.do_peak_picking == 'OSW-PyProphet':
if peak_picking_settings.do_peak_picking == 'Feature File Boundaries':
with time_block() as elapsed_time:
tr_group_feature_data = self.xic_data.loadTransitionGroupFeatures(transition_list_ui.transition_settings.selected_peptide, transition_list_ui.transition_settings.selected_charge)
st.write(f"Loading OSW-PyProphet Peak Boundaries... Elapsed time: {elapsed_time()}")
st.write(f"Loading Feature File Peak Boundaries... Elapsed time: {elapsed_time()}")
elif peak_picking_settings.do_peak_picking == 'pyPeakPickerMRM':
with time_block() as elapsed_time:
# Peak picking using pyMRMTransitionGroupPicker
Expand Down
6 changes: 3 additions & 3 deletions massdash/server/PeakPickingServer.py
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Expand Up @@ -35,7 +35,7 @@ def __init__(self, peak_picking_settings: PeakPickingUISettings, chrom_plot_sett

def perform_osw_pyprophet_peak_picking(self, xic_data: SqMassLoader, transition_list_ui: Literal['ExtractedIonChromatogramAnalysisUI', 'RawTargetedExtractionAnalysisUI']):
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I am having difficulties with this method in the GUI could you please look into this? I think that the loader object for the raw data is not currently being passed which causes loadTransitionGroupFeature to fail. Not sure what the best way to solve this without just adding more arguments

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You're getting this error?

AttributeError: 'NoneType' object has no attribute 'loadTransitionGroupFeature'

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yes thats the error. I think it is because there is no XIC data/loader object passed

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I passed the mzml loader object now instead to get the feature data from the results file. I think I initially used the sqMass workflow that's why it failed.

"""
Performs peak picking using OSW-PyProphet algorithm.
Get peak boundaries from Feature File Boundaries.

Args:
xic_data (object): The XIC data.
Expand All @@ -49,7 +49,7 @@ def perform_osw_pyprophet_peak_picking(self, xic_data: SqMassLoader, transition_
transition_list_ui.transition_settings.selected_peptide,
transition_list_ui.transition_settings.selected_charge
)
st.write(f"Loading OSW-PyProphet Peak Boundaries... Elapsed time: {elapsed_time()}")
st.write(f"Loading Feature File Peak Boundaries... Elapsed time: {elapsed_time()}")
return tr_group_feature_data

def perform_pypeakpicker_mrm_peak_picking(self, tr_group_data: TransitionGroup):
Expand Down Expand Up @@ -118,7 +118,7 @@ def perform_peak_picking(self, tr_group_data: TransitionGroup=None, xic_data: Sq
tr_group_feature_data = {}

# Perform peak picking based on the selected method
if self.peak_picking_settings.do_peak_picking == 'OSW-PyProphet':
if self.peak_picking_settings.do_peak_picking == 'Feature File Boundaries':
tr_group_feature_data = self.perform_osw_pyprophet_peak_picking(xic_data, transition_list_ui)
elif self.peak_picking_settings.do_peak_picking == 'pyPeakPickerMRM':
tr_group_feature_data = self.perform_pypeakpicker_mrm_peak_picking(tr_group_data)
Expand Down
4 changes: 2 additions & 2 deletions massdash/ui/PeakPickingUISettings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,7 @@ def create_ui(self, plot_settings: ChromatogramPlotUISettings):
st.sidebar.title("Peak Picking")

## Perform Peak Picking
self.do_peak_picking = st.sidebar.selectbox("Peak Picking", ['none', 'OSW-PyProphet', 'pyPeakPickerMRM', 'MRMTransitionGroupPicker', 'Conformer'], help="Peak picking method to use.")
self.do_peak_picking = st.sidebar.selectbox("Peak Picking", ['none', 'Feature File Boundaries', 'pyPeakPickerMRM', 'MRMTransitionGroupPicker', 'Conformer'], help="Peak picking method to use.")

if self.do_peak_picking != 'none':
## Perform peak picking on displayed chromatogram, or adjust smoothing separately for peak picking?
Expand All @@ -54,7 +54,7 @@ def create_ui(self, plot_settings: ChromatogramPlotUISettings):
if self.do_peak_picking == "pyPeakPickerMRM":
self.peak_picker_algo_settings = pyPeakPickerMRMUISettings(self)
self.peak_picker_algo_settings.create_ui(plot_settings)
elif self.do_peak_picking == "OSW-PyProphet":
elif self.do_peak_picking == "Feature File Boundaries":
pass
elif self.do_peak_picking == "MRMTransitionGroupPicker":
self.peak_picker_algo_settings = MRMTransitionGroupPickerUISettings(self)
Expand Down
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