From f0f7edf152f34b92325102c0a5c2034ffec29d1d Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Sat, 21 Sep 2019 12:08:36 +0200
Subject: [PATCH] Python API: small option improvements

---
 python/obitools3/apps/optiongroups/__init__.py |  9 ++++++++-
 python/obitools3/commands/alignpairedend.pyx   | 10 +++++-----
 python/obitools3/commands/uniq.pyx             |  6 +++++-
 3 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/python/obitools3/apps/optiongroups/__init__.py b/python/obitools3/apps/optiongroups/__init__.py
index 6dbd250..94171e3 100755
--- a/python/obitools3/apps/optiongroups/__init__.py
+++ b/python/obitools3/apps/optiongroups/__init__.py
@@ -222,8 +222,11 @@ def __addDMSOutputOption(optionManager):
     group.add_argument('--no-create-dms',
                  action="store_true", dest="obi:nocreatedms",
                  default=False,
-                 help="Don't create an output DMS is it is not existing")
+                 help="Don't create an output DMS it does not already exist")
 
+
+def __addEltLimitOption(optionManager):
+    group = optionManager.add_argument_group("Option to limit the number of elements per line in columns")
     group.add_argument('--max-elts',
                  action="store", dest="obi:maxelts",
                  metavar='<N>',
@@ -306,3 +309,7 @@ def addAllOutputOption(optionManager):
 def addNoProgressBarOption(optionManager):
     __addNoProgressBarOption(optionManager)
     
+def addEltLimitOption(optionManager):
+    __addEltLimitOption(optionManager)
+    
+    
\ No newline at end of file
diff --git a/python/obitools3/commands/alignpairedend.pyx b/python/obitools3/commands/alignpairedend.pyx
index 2530f63..6a1bd97 100755
--- a/python/obitools3/commands/alignpairedend.pyx
+++ b/python/obitools3/commands/alignpairedend.pyx
@@ -45,17 +45,17 @@ def addOptions(parser):
                      type=float,
                      help="Minimum score for keeping alignments")
 
-    group.add_argument('-A', '--true-ali',
-                       action="store_true", dest="alignpairedend:trueali",
-                       default=False,
-                       help="Performs gap free end alignment of sequences instead of using kmers to compute alignments (slower).")
+#     group.add_argument('-A', '--true-ali',
+#                        action="store_true", dest="alignpairedend:trueali",
+#                        default=False,
+#                        help="Performs gap free end alignment of sequences instead of using kmers to compute alignments (slower).")
 
     group.add_argument('-k', '--kmer-size',
                        action="store", dest="alignpairedend:kmersize",
                        metavar="#",
                        default=3,
                        type=int,
-                       help="K-mer size for kmer comparisons, between 1 and 4 (not when using -A option; default: 3)")
+                       help="K-mer size for kmer comparisons, between 1 and 4 (default: 3)")
 
 
 la = QSolexaReverseAssemble()
diff --git a/python/obitools3/commands/uniq.pyx b/python/obitools3/commands/uniq.pyx
index 5bad7a2..c0c437a 100644
--- a/python/obitools3/commands/uniq.pyx
+++ b/python/obitools3/commands/uniq.pyx
@@ -10,7 +10,10 @@ from obitools3.dms.column.column cimport Column, Column_line
 from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN, TAXID_COLUMN, \
                                         TAXID_DIST_COLUMN, MERGED_TAXID_COLUMN, MERGED_COLUMN, MERGED_PREFIX
 from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t
-from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption, addTaxonomyOption
+from obitools3.apps.optiongroups import addMinimalInputOption, \
+                                        addMinimalOutputOption, \
+                                        addTaxonomyOption, \
+                                        addEltLimitOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.utils cimport tobytes, tostr
@@ -27,6 +30,7 @@ def addOptions(parser):
     addMinimalInputOption(parser)
     addTaxonomyOption(parser)
     addMinimalOutputOption(parser)
+    addEltLimitOption(parser)
  
     group = parser.add_argument_group('obi uniq specific options')