From f54e2750986260e74512fc7f1de26e0145dc3632 Mon Sep 17 00:00:00 2001
From: Ivan Blagoev Topolsky <ivan.topolsky@sib.swiss>
Date: Fri, 5 Jul 2024 18:13:20 +0200
Subject: [PATCH] [bugfix] filters: empty cli option and quotes

- supports `lollipop deconvolute  --filters="" ...` to skip filters
- supports statement with quotes around column `- "column" == val`
---
 lollipop/cli/deconvolute.py | 2 ++
 lollipop/preprocessors.py   | 6 +++---
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/lollipop/cli/deconvolute.py b/lollipop/cli/deconvolute.py
index 47bce76..5c94fe4 100755
--- a/lollipop/cli/deconvolute.py
+++ b/lollipop/cli/deconvolute.py
@@ -151,6 +151,8 @@ def deconvolute(
             filters = yaml.load(file)
 
         print(f"{len(filters)} filter{ '' if len(filters) == 1 else 's' } loaded")
+    else:
+        filters = None
 
     # data
     try:
diff --git a/lollipop/preprocessors.py b/lollipop/preprocessors.py
index 3702140..62af257 100644
--- a/lollipop/preprocessors.py
+++ b/lollipop/preprocessors.py
@@ -121,15 +121,15 @@ def general_preprocess(
 
     def filter_mutations(self, filters=None):
         """filter out hardcoded problematic mutations"""
-        if filters is None:
+        if not filters:
             return self
 
         types = self.df_tally.dtypes
 
         rxprser = re.compile(
-            r"^ *(?:(?P<col>"
+            r"^ *(?P<qc>['\"]?)(?:(?P<col>"
             + r"|".join(self.df_tally.columns)
-            + r")|(?P<bad>\w+)) *(?P<op>in|[<>=~!]*) *(?P<qv>['\"]?)(?P<val>.+)(?P=qv) *$"
+            + r")|(?P<bad>\w+))(?P=qc) *(?P<op>in|[<>=~!]*) *(?P<qv>['\"]?)(?P<val>.+)(?P=qv) *$"
         )
 
         def apply_filter_statement(name, fs):