controls working

src/submissions/backend/excel/__init__.py

@@ -0,0 +1,43 @@
+
+from pandas import DataFrame
+import re
+
+
+
+def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
+    """
+    _summary_
+
+    Args:
+        df (DataFrame): _description_
+        column_name (str): _description_
+
+    Returns:
+        list: _description_
+    """    
+    return sorted(df[column_name].unique())
+
+
+def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
+    """
+    Removes semi-duplicates from dataframe after finding sequencing repeats.
+
+    Args:
+        settings (dict): settings passed down from click
+        df (DataFrame): initial dataframe
+
+    Returns:
+        DataFrame: dataframe with originals removed in favour of repeats.
+    """    
+    sample_names = get_unique_values_in_df_column(df, column_name="name")
+    if 'rerun_regex' in ctx:
+        # logger.debug(f"Compiling regex from: {settings['rerun_regex']}")
+        rerun_regex = re.compile(fr"{ctx['rerun_regex']}")
+        for sample in sample_names:
+            # logger.debug(f'Running search on {sample}')
+            if rerun_regex.search(sample):
+                # logger.debug(f'Match on {sample}')
+                first_run = re.sub(rerun_regex, "", sample)
+                # logger.debug(f"First run: {first_run}")
+                df = df.drop(df[df.name == first_run].index)
+        return df