From 3af856c93139b60086bc53be3853b6512d712ebb Mon Sep 17 00:00:00 2001
From: Florian Plaza Onate <florian.plaza-onate@inrae.fr>
Date: Tue, 2 Apr 2024 15:07:40 +0000
Subject: [PATCH] Hide feature not implemented

---
 meteor/meteor.py | 52 +++++++++++++++++++++++++-----------------------
 1 file changed, 27 insertions(+), 25 deletions(-)

diff --git a/meteor/meteor.py b/meteor/meteor.py
index 8ec2ec1..3388eb1 100644
--- a/meteor/meteor.py
+++ b/meteor/meteor.py
@@ -460,13 +460,13 @@ def get_arguments() -> Namespace:  # pragma: no cover
         help="Remove samples with no detected species (MSPs) "
         "(default: %(default)s).",
     )
-    merging_parser.add_argument(
-        "-m",
-        dest="output_mpa",
-        action="store_true",
-        help="Save the merged species abundance table in the style of MetaPhlan "
-        "(default: %(default)s).",
-    )
+    #merging_parser.add_argument(
+    #    "-m",
+    #    dest="output_mpa",
+    #    action="store_true",
+    #    help="Save the merged species abundance table in the style of MetaPhlan "
+    #    "(default: %(default)s).",
+    #)
     merging_parser.add_argument(
         "-b",
         dest="output_biom",
@@ -474,22 +474,22 @@ def get_arguments() -> Namespace:  # pragma: no cover
         help="Save the merged species abundance table in biom format "
         "(default: %(default)s).",
     )
-    merging_parser.add_argument(
-        "--tax_lev",
-        dest="taxonomic_level",
-        default=Merging.DEFAULT_MPA_TAXONOMIC_LEVEL,
-        choices=Merging.MPA_TAXONOMIC_LEVELS,
-        help="""The taxonomic level for mpa output (default: %(default)s):
-                        'a' : all taxonomic levels
-                        'k' : kingdoms
-                        'p' : phyla only
-                        'c' : classes only
-                        'o' : orders only
-                        'f' : families only
-                        'g' : genera only
-                        's' : species only
-                        't' : MSPs only""",
-    )
+    #merging_parser.add_argument(
+    #    "--tax_lev",
+    #    dest="taxonomic_level",
+    #    default=Merging.DEFAULT_MPA_TAXONOMIC_LEVEL,
+    #    choices=Merging.MPA_TAXONOMIC_LEVELS,
+    #    help="""The taxonomic level for mpa output (default: %(default)s):
+    #                    'a' : all taxonomic levels
+    #                    'k' : kingdoms
+    #                    'p' : phyla only
+    #                    'c' : classes only
+    #                    'o' : orders only
+    #                    'f' : families only
+    #                    'g' : genera only
+    #                    's' : species only
+    #                    't' : MSPs only""",
+    #)
     merging_parser.add_argument(
         "-o",
         dest="merging_dir",
@@ -782,8 +782,10 @@ def main() -> None:  # pragma: no cover
             args.min_msp_abundance,
             args.min_msp_occurrence,
             args.remove_sample_with_no_msp,
-            args.output_mpa,
-            args.taxonomic_level,
+            None,
+            None,
+            #args.output_mpa,
+            #args.taxonomic_level,
             args.output_biom,
             args.output_gene_matrix,
         )