From da48a9d1af85b2cbdf8fa112c47fa858b3ab9d20 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Fri, 28 Jul 2017 09:36:18 +0200
Subject: [PATCH] Patch group of option : types must be callable not a string

---
 python/obitools3/apps/optiongroups/__init__.py | 14 +++++++-------
 python/obitools3/commands/grep.pyx             |  4 ++--
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/python/obitools3/apps/optiongroups/__init__.py b/python/obitools3/apps/optiongroups/__init__.py
index 6cb8426..38e68b5 100644
--- a/python/obitools3/apps/optiongroups/__init__.py
+++ b/python/obitools3/apps/optiongroups/__init__.py
@@ -13,14 +13,14 @@ def __addInputOption(optionManager):
                      action="store", dest="obi:skip",
                      metavar='<N>',
                      default=None,
-                     type='int',
+                     type=int,
                      help="skip the N first sequences")
 
     group.add_argument('--only',
                      action="store", dest="obi:only",
                      metavar='<N>',
                      default=None,
-                     type='int',
+                     type=int,
                      help="treat only N sequences")
 
 
@@ -115,19 +115,19 @@ def __addTabularInputOption(optionManager):
     group.add_argument('--sep',
                      action="store", dest="obi:sep",
                      default=None,
-                     type="bytes",
+                     type=bytes,
                      help="Column separator")
     
     group.add_argument('--dec',
                      action="store", dest="obi:dec",
                      default=b".",
-                     type="bytes",
+                     type=bytes,
                      help="Decimal separator")
     
     group.add_argument('--na-string',
                      action="store", dest="obi:nastring",
                      default=b"NA",
-                     type="bytes",
+                     type=bytes,
                      help="String associated to Non Available (NA) values")
     
     group.add_argument('--strip-white',
@@ -143,10 +143,10 @@ def __addTabularInputOption(optionManager):
     group.add_argument('--comment-char',
                      action="store", dest="obi:commentchar",
                      default=b"#",
-                     type="bytes",
+                     type=bytes,
                      help="Lines starting by this char are considered as comment")
   
-def addMinimalOption(optionManager):
+def addMinimalInputOption(optionManager):
     __addInputOption(optionManager)
     
 def addSequenceInputOption(optionManager):
diff --git a/python/obitools3/commands/grep.pyx b/python/obitools3/commands/grep.pyx
index 8a1d292..1e01710 100644
--- a/python/obitools3/commands/grep.pyx
+++ b/python/obitools3/commands/grep.pyx
@@ -5,7 +5,7 @@ from obitools3.dms.dms import DMS       # TODO cimport doesn't work
 from obitools3.dms.view.view import View, Line_selection    # TODO cimport doesn't work
  
  
-from obitools3.apps.optiongroups import addInputOption
+from obitools3.apps.optiongroups import addSequenceInputOption
 from functools import reduce
 import time
  
@@ -18,7 +18,7 @@ default_config = {   'inputview'    : None,
  
 def addOptions(parser):
     
-    addInputOption(parser)
+    addSequenceInputOption(parser)
  
     # TODO put this common group somewhere else but I don't know where
     group=parser.add_argument_group('DMS and view options')