--from-taxid and --from-taxtable are now --from-id and --from-table

fhcrc · Sep 21, 2016 · 7fdc05d · 7fdc05d
1 parent 7ba03ec
commit 7fdc05d
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Showing 2 changed files with 16 additions and 16 deletions.
diff --git a/taxtastic/subcommands/taxtable.py b/taxtastic/subcommands/taxtable.py
@@ -61,13 +61,13 @@ def build_parser(parser):
         help='Name of the sqlite database file')
 
     parser.add_argument(
-        '--from-taxtable',
+        '--from-table',
         metavar='CSV',
         help=('taxtable to derive new taxtable from'))
     parser.add_argument(
         '--full',
         action='store_true',
-        help='Show all ranks in output file.')
+        help='Include rank columns not in final lineages.')
 
     input_group = parser.add_argument_group('input options')
 
@@ -96,7 +96,7 @@ def build_parser(parser):
         field "tax_id" """)
 
     input_group.add_argument(
-        '--from-taxid',
+        '--from-id',
         help=('taxid to branch from'))
 
     output_group = parser.add_argument_group(
@@ -119,9 +119,9 @@ def action(args):
     ranks = pandas.read_sql_table('ranks', engine, index_col='index')
     ranks = ranks['rank'].tolist()
 
-    if args.from_taxtable:
-        log.info('using taxtable ' + args.from_taxtable)
-        taxtable = pandas.read_csv(args.from_taxtable, dtype=str).set_index('tax_id')
+    if args.from_table:
+        log.info('using taxtable ' + args.from_table)
+        taxtable = pandas.read_csv(args.from_table, dtype=str).set_index('tax_id')
     else:
         log.info('building taxtable from ' + args.database_file)
         nodes = pandas.read_sql_table('nodes', engine, index_col='tax_id')
@@ -132,13 +132,13 @@ def action(args):
         nodes = nodes.join(names['tax_name'])
         taxtable = build_taxtable(nodes, ranks)
 
-    if args.from_taxid:
-        from_taxon = taxtable.loc[args.from_taxid]
+    if args.from_id:
+        from_taxon = taxtable.loc[args.from_id]
 
-        # select all rows where rank column == args.from_taxid
-        from_table = taxtable[taxtable[from_taxon['rank']] == args.from_taxid]
+        # select all rows where rank column == args.from_id
+        from_table = taxtable[taxtable[from_taxon['rank']] == args.from_id]
 
-        # build taxtable up to root from args.from_taxid
+        # build taxtable up to root from args.from_id
         while from_taxon.name != '1':  # root
             parent = taxtable.loc[from_taxon['parent_id']]
             from_table = pandas.concat([pandas.DataFrame(parent).T, from_table])
@@ -252,6 +252,6 @@ def build_taxtable(df, ranks):
                 how='inner')
             lineages = lineages.append(at_rank)
 
-        sys.stderr.write('built {} of {} rank lineages\r'.format(i, rank_count))
+        sys.stderr.write('{} of {} rank lineages completed\r'.format(i, rank_count))
 
     return lineages.drop('rank_parent', axis=1).set_index(df_index_name)
diff --git a/tests/test_subcommands.py b/tests/test_subcommands.py
@@ -275,8 +275,8 @@ class _Args(object):
                     verbosity = 0
                     out_file = h
                     full = False
-                    from_taxtable = None
-                    from_taxid = None
+                    from_table = None
+                    from_id = None
                 self.assertNotEqual(taxtable.action(_Args()), 0)
 
     def test_seqinfo(self):
@@ -290,8 +290,8 @@ class _Args(object):
                 out_file = tf
                 verbosity = 0
                 full = False
-                from_taxtable = None
-                from_taxid = None
+                from_table = None
+                from_id = None
             self.assertIsNone(taxtable.action(_Args()))
             # No output check at present
             self.assertTrue(tf.tell() > 0)