comparison process_intensities.xml @ 4:5d541df02496 draft

planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/mti-utils commit 5cf3005f482381216061eb8718aba8f5c8bcb0d5

3:4f5abe01531c

#if $AF_method.select_method == 'SBR':
AF_markers = [x for x in list(marker_df['${AF_method.AF_col}'].unique()) if x != 'None']
print(f'Detected {quant[AF_markers].eq(0.0).any(axis=1).sum()} cells with AF values of zero in the dataset')

#if $AF_filter == 'filter':
pre_filter_count = len(quant)
quant = quant.loc[quant[AF_markers].ne(0.0).any(axis=1),:]
print(f'Filtered out {pre_filter_count - len(quant)} cells that had AF values of 0.0')

#elif $AF_filter == 'clip':
print('Clipping all AF values equal to 0.0 to the minimum non-zero AF value')
for af in AF_markers:
    quant[af] = quant[af].clip(lower = quant[af][quant[af].ne(0.0)].min())

#end if

4:5d541df02496

#if $AF_method.select_method == 'SBR':
AF_markers = [x for x in list(marker_df['${AF_method.AF_col}'].unique()) if x != 'None']
print(f'Detected {quant[AF_markers].eq(0.0).any(axis=1).sum()} cells with AF values of zero in the dataset')

#if $AF_method.AF_filter == 'filter':
pre_filter_count = len(quant)
quant = quant.loc[quant[AF_markers].ne(0.0).any(axis=1),:]
print(f'Filtered out {pre_filter_count - len(quant)} cells that had AF values of 0.0')

#elif $AF_method.AF_filter == 'clip':
print('Clipping all AF values equal to 0.0 to the minimum non-zero AF value')
for af in AF_markers:
    quant[af] = quant[af].clip(lower = quant[af][quant[af].ne(0.0)].min())

#end if