more verbose

barcode_validator/taxonomy.py

@@ -103,15 +103,15 @@ def collect_lineages(taxids, tree):
             logging.debug(f'Found tip {tip.name} with taxid {taxid}')
     logging.info(f'Found {len(tips)} tips for {len(taxids)} in the tree')
     for tip in tips:
-        lineage = []
+        lineage = set()
         for node in tree.root.get_path(tip):
             logging.debug(f'Traversing {node} from lineage {tip}')
             if node.taxonomic_rank == str(config.get('level')).lower():
-                lineage.append(node.name)
+                lineage.update(node.name)
                 logging.info(f'Found ancestor {node} for {tip.name}')
         lineages.append(lineage)
-    logging.info(f'Collected {len(lineages)} lineages')
-    return lineages
+    logging.info(f'Collected {len(lineages)} distinct lineages')
+    return list(lineages)
 
 
 def run_blast(sequence):

config/config.yml

@@ -34,7 +34,7 @@ ncbi_taxonomy: /home/rutger.vos/data/ncbi/taxdump/taxdump.tar.gz
 
 # Configuration for logging. The verbosity level specified here is overridden by the value provided on the command
 # line with the -v/-verbosity argument. The log file is written to the current working directory.
-log_level: INFO
+log_level: DEBUG
 log_file: ../log_file.log
 
 # Which translation table is used. This value is an integer that corresponds to the tables used by NCBI and parsed