update

src/metatag/database/labelparsers.py

@@ -8,8 +8,6 @@
 import re
 import warnings
 
-import pandas as pd
-
 
 class LabelParser:
     def __init__(self, label: str) -> None:
@@ -38,7 +36,7 @@ def extract_genome_id(self) -> str:
         else:
             genome_id = self.extract_oceanmicrobiome_id()
         return genome_id
-    
+
     def extract_mmp_id(self) -> str:
         """Extract MMP ID from sequence label
 
@@ -50,7 +48,7 @@ def extract_mmp_id(self) -> str:
             return re.search(db_entry, self._label).group(0).strip("_")
         except Exception:
             return ""
-        
+
     def extract_taxid(self) -> str:
         """Extract NCBI taxon ID from sequence label
 
@@ -62,11 +60,11 @@ def extract_taxid(self) -> str:
             return f"taxid_{re.search(db_entry, self._label).group(2)}"
         except Exception:
             return ""
-        
+
     def extract_oceanmicrobiome_id(self) -> str:
         """Extract OceanMicrobiome ID from sequence label
 
         Returns:
             str: OceanMicrobiome ID
         """
-        return "_".join(self._label.split("_")[:4])
+        return "_".join(self._label.split("_")[:4])

src/metatag/pipelines.py

@@ -23,6 +23,7 @@
 
 logger = logging.getLogger(__name__)
 
+
 class ReferenceTreeBuilder:
     """
     Reconstruct reference phylogenetic tree from sequence database and hmms
@@ -152,7 +153,9 @@ def run(self) -> None:
             )
             preprocess.run(preprocess_args)
         if not self._out_cleaned_database.exists():
-            logger.error("Please, first run preprocess step by setting 'skip_preprocess=False'.")
+            logger.error(
+                "Please, first run preprocess step by setting 'skip_preprocess=False'."
+            )
 
         database_args = CommandArgs(
             data=self._out_cleaned_database,
@@ -441,7 +444,7 @@ def placements_tree(self) -> Path:
     def taxtable(self) -> Path:
         """Path to output file with taxonomic assignments."""
         return self._out_taxtable
-    
+
     @property
     def query_labels(self) -> Path:
         """Path to output file with query labels."""