diff customizemetadata.py @ 5:6dee4abadccb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6

--- a/customizemetadata.py	Wed Feb 02 22:03:11 2022 +0000
+++ b/customizemetadata.py	Sat Dec 03 10:43:21 2022 +0000
@@ -56,6 +56,7 @@
         'taxonomy': in_metadata['taxonomy'],
         'merged_taxon': {}
     }
+
     # transform merged_taxons tuple keys to string
     for k in in_metadata['merged_taxon']:
         n = ' , '.join(k)
@@ -85,6 +86,13 @@
         n = ' , '.split(k)
         out_metadata[n] = in_metadata['merged_taxon'][k]
 
+    # Ensure that there are 8 taxonomy levels (for compatibility between Metaphlan v3 and v4)
+    # v3 DB release encodes the taxids as: ('2|1224|1236|91347|543|547|354276', 4404432)
+    # v4 DB release encodes the taxids as: ('2|1224|1236|91347|543|547|354276|', 4404432)
+    for k in out_metadata['taxonomy']:
+        if out_metadata['taxonomy'][k][0].count('|') == 6:
+            out_metadata['taxonomy'][k] = (out_metadata['taxonomy'][k][0] + '|', out_metadata['taxonomy'][k][1])
+
     # dump metadata to Pickle file
     with bz2.BZ2File(pkl_fp, 'w') as pkl_f:
         pickle.dump(out_metadata, pkl_f)