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Fixes 459: Add popEVE gap frequency filtering #460

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Fixes 459: Add popEVE gap frequency filtering #460

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12 changes: 9 additions & 3 deletions mavisp/modules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1820,16 +1820,22 @@ def ingest(self, mutations):
try:

popeve_df = pd.read_csv(os.path.join(self.data_dir, self.module_dir, popeve_file),
usecols=['mutant', 'popEVE'],
usecols=['mutant', 'popEVE', 'gap frequency'],
dtype={ 'mutant' : 'string',
'popEVE' : 'float32'},
'popEVE' : 'float32',
'gap frequency' :'float32'},
index_col='mutant')
except Exception as e:
this_error = f"Exception {type(e).__name__} occurred when parsing the csv files. Arguments:{e.args}"
raise MAVISpMultipleError(warning=warnings,
critical=[MAVISpCriticalError(this_error)])

popeve_df.loc[
popeve_df['gap frequency'] >= 0.5,
'popEVE'
] = pd.NA

self.data = popeve_df.rename(columns = {'popEVE' : 'popEVE score'})
self.data = popeve_df.rename(columns = {'popEVE' : 'popEVE score'}).drop(columns = ['gap frequency'])

if len(warnings) > 0:
raise MAVISpMultipleError(warning=warnings,
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2 changes: 1 addition & 1 deletion test_data/mavisp_web_server/dataset_info.csv
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Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
Date of run,Number of mutations,Number of proteins,Number of proteins in simple mode only,Number of proteins in ensemble mode only,Number of proteins in both modes
2026-04-28,3781,1,0,0,1
2026-05-12,3781,1,0,0,1