without pruning

taxtastic/subcommands/taxtable.py

@@ -125,9 +125,6 @@ def action(args):
     else:
         log.info('building taxtable from ' + args.database_file)
         nodes = pandas.read_sql_table('nodes', engine, index_col='tax_id')
-        if args.from_taxid:
-            log.info('pruning nodes above taxid ' + args.from_taxid)
-            nodes = prune_nodes(nodes, ranks, nodes.loc[args.from_taxid])
         names = pandas.read_sql_table(
             'names', engine, columns=['tax_id', 'tax_name', 'is_primary'])
         names = names[names['is_primary']].set_index('tax_id')
@@ -258,20 +255,3 @@ def build_taxtable(df, ranks):
         sys.stderr.write('built {} of {} rank lineages\r'.format(i, rank_count))
 
     return lineages.drop('rank_parent', axis=1).set_index(df_index_name)
-
-
-def prune_nodes(nodes, ranks, from_node):
-    keep = from_node.name
-    keep_ids = set(['1', keep])  # root, keep
-    while keep != '1':
-        keep_ids.add(keep)
-        keep = nodes.loc[keep]['parent_id']
-
-    # remove nodes in upper ranks
-    rank = from_node['rank']
-    drop_ids = set()
-    for r in ranks[:ranks.index(rank)]:
-        idrop = ((nodes['rank'] == r) & (~nodes.index.isin(keep_ids)))
-        drop_ids.update(nodes[idrop].index)
-
-    return nodes.drop(drop_ids)