added utils.py for create logger

biocore · Sep 5, 2024 · 96b1e85 · 96b1e85
1 parent af377ba
commit 96b1e85
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Showing 2 changed files with 15 additions and 1 deletion.
diff --git a/micov/_utils.py 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
diff --git 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]