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Add configurable LOG_INTERVAL for protein processing logs #80

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Add configurable LOG_INTERVAL for protein processing logs #80

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1b18b12
Add configurable LOG_INTERVAL for protein processing logs
GeorgWa Dec 22, 2025
72794e1
Merge main and resolve conflicts
GeorgWa Dec 22, 2025
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6 changes: 6 additions & 0 deletions directlfq/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,12 @@ def set_log_processed_proteins(log_processed_proteins = True):
global LOG_PROCESSED_PROTEINS
LOG_PROCESSED_PROTEINS = log_processed_proteins

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Copilot AI Dec 22, 2025

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The separator comment uses inconsistent formatting compared to other separators in the file. The separator at line 23 uses the same format, but the separator at line 16 appears after the function definition instead of before the variable declaration like line 23. Consider moving this separator to line 15 to maintain consistency with the existing pattern where separators precede variable declarations.

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##########################
LOG_INTERVAL = 100

def set_log_interval(log_interval = 100):
global LOG_INTERVAL
LOG_INTERVAL = log_interval

##########################
PROTEIN_ID = 'protein'
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2 changes: 1 addition & 1 deletion directlfq/protein_intensity_estimation.py
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Expand Up @@ -126,7 +126,7 @@ def calculate_peptide_and_protein_intensities(idx, peptide_intensity_df, num_sam
if len(peptide_intensity_df.index) > 1:
peptide_intensity_df = ProtvalCutter(peptide_intensity_df, maximum_df_length=100).get_dataframe()

if(idx%100 ==0) and config.LOG_PROCESSED_PROTEINS:
if(idx % config.LOG_INTERVAL == 0) and config.LOG_PROCESSED_PROTEINS:
LOGGER.info(f"lfq-object {idx}")
summed_pepint = np.nansum(2**peptide_intensity_df)

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