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114 produce clearer error logs when small variant tables are empty #115

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Merged
marrip merged 3 commits into from
Jun 11, 2026
Merged

114 produce clearer error logs when small variant tables are empty #115

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a8c9106
fix: add safeguard to avoid ZeroDivisionError
marrip Jun 10, 2026
8a0c267
fix: avoid unspecific error when file is empty
marrip Jun 10, 2026
0df70fc
feat: replace X suffix of protein changes with asterisk
marrip Jun 10, 2026
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16 changes: 14 additions & 2 deletions Script/PRONTO.py
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Original file line number Diff line number Diff line change
Expand Up @@ -739,13 +739,21 @@ def insert_table_to_ppt(table_file,slide_n,table_name,left_h,top_h,width_h,left_
# round floats to 2 decimal places
table_data = pronto.set_column_to_2_decimals(table_data, "AF_tumor_DNA")

# replace X suffix with *
if "Protein_change_short" in table_data.columns:
table_data["Protein_change_short"] = table_data["Protein_change_short"].str.replace(r'X$', '*', regex=True)

# determine column and row number
cols = len(table_header)
rows = len(table_data)

# how many slides are required
if not table_max_rows_per_slide:
table_max_rows_per_slide = rows
if rows == 0:
logging.warning("{} is empty".format(table_file))
return
else:
table_max_rows_per_slide = rows
total_slides_needed = math.ceil(rows / table_max_rows_per_slide)

# Add data to ppt
Expand Down Expand Up @@ -1351,7 +1359,11 @@ def main(argv):
topfilters = pronto.parse_topfilter(cfg, output_file_preMTB_table_path)
for filter in topfilters:
for filter_column in filter['filter_columns']:
small_variant_data = pandas.read_csv(data_file_small_variant_table, sep='\t', comment='#')
try:
small_variant_data = pandas.read_csv(data_file_small_variant_table, sep='\t', comment='#')
except pandas.errors.EmptyDataError:
logging.warning("{} is empty".format(data_file_small_variant_table))
sys.exit(1)
try:
small_variant_data = pronto.filter_small_variant_data(small_variant_data, DNA_sampleID, filter_column, filter['key_word'])
except ValueError:
Expand Down
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