From 96b1e85e428559ceced4ed82b48f184752b4a59e Mon Sep 17 00:00:00 2001
From: sherlyn99 <y1weng@ucsd.edu>
Date: Thu, 5 Sep 2024 13:36:32 -0700
Subject: [PATCH] added utils.py for create logger

---
 micov/_utils.py | 12 ++++++++++++
 micov/cli.py    |  4 +++-
 2 files changed, 15 insertions(+), 1 deletion(-)
 create mode 100644 micov/_utils.py

diff --git a/micov/_utils.py b/micov/_utils.py
new file mode 100644
index 0000000..251f7ed
--- /dev/null
+++ b/micov/_utils.py
@@ -0,0 +1,12 @@
+import logging
+
+def configure_logging():
+    logger = logging.getLogger("micov")
+    logger.setLevel(logging.INFO)
+    # Check if the logger already has handlers (prevents adding multiple handlers)
+    if not logger.hasHandlers():
+        handler = logging.StreamHandler()
+        formatter = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s: %(message)s")
+        handler.setFormatter(formatter)
+        logger.addHandler(handler)
+    return logger
\ No newline at end of file
diff --git a/micov/cli.py b/micov/cli.py
index 9e8643d..a4ee61f 100644
--- a/micov/cli.py
+++ b/micov/cli.py
@@ -109,7 +109,9 @@ def compress(data, output, disable_compression, lengths, taxonomy):
             taxonomy = parse_taxonomy(taxonomy)
 
     if os.path.isdir(data):
-        file_list = glob(data + "/*.sam") + glob(data + '/*.sam.xz') + glob(data + '/*.sam.gz')
+        file_list = (glob(data + "/*.sam") 
+                    + glob(data + '/*.sam.xz') 
+                    + glob(data + '/*.sam.gz'))
     else:
         file_list = [data]