fine tuning

workflow/scripts/coverage_table.py

@@ -1,7 +1,15 @@
 import pandas as pd
+import numpy as np
 
 sys.stderr = open(snakemake.log[0], "w")
 
+
+def add_missing_columns(df, samples):
+    missing_columns = set(samples).difference(df.columns)
+    df[list(missing_columns)] = np.nan
+    return df
+
+
 group_regions = dict()
 samples = []
 for bed in snakemake.input:
@@ -23,6 +31,7 @@
     df = pd.DataFrame.from_dict(group_regions).T
     df.index.names = ("chromosome", "gene")
     df.reset_index(inplace=True)
+    df = add_missing_columns(samples)
 else:
     df = pd.DataFrame(columns=["chromosome", "gene"] + samples)