From b93b982a18eef567e5fd3f0b7fac04d6bb738b63 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 13 Dec 2017 22:25:15 +0100
Subject: [PATCH] Cython: added an option for input taxdump and and an option
 for the maximum number of elements in columns with multiple elements per line

---
 .../obitools3/apps/optiongroups/__init__.py   | 25 +++++++++++++++++--
 1 file changed, 23 insertions(+), 2 deletions(-)

diff --git a/python/obitools3/apps/optiongroups/__init__.py b/python/obitools3/apps/optiongroups/__init__.py
index 23fb375..27f7b1b 100644
--- a/python/obitools3/apps/optiongroups/__init__.py
+++ b/python/obitools3/apps/optiongroups/__init__.py
@@ -154,7 +154,15 @@ def __addTaxonomyInputOption(optionManager):
                      help="Taxonomy URI")
     
     #TODO option bool to download taxo if URI doesn't exist
-    
+
+def __addTaxdumpInputOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for taxdump")
+
+    group.add_argument('--taxdump',
+                     action="store", dest="obi:taxdump",
+                     default=None,
+                     help="Taxdump path")
+
 def addMinimalInputOption(optionManager):
     __addInputOption(optionManager)
     
@@ -169,12 +177,15 @@ def addTabularInputOption(optionManager):
 def addTaxonomyInputOption(optionManager):
     __addTaxonomyInputOption(optionManager)
 
+def addTaxdumpInputOption(optionManager):
+    __addTaxdumpInputOption(optionManager)
+
 def addAllInputOption(optionManager):
     __addInputOption(optionManager)
     __addSequenceInputOption(optionManager)
     __addTabularInputOption(optionManager)
     __addTaxonomyInputOption(optionManager)
-    
+    __addTaxdumpInputOption(optionManager)    
     
 def __addOutputOption(optionManager):
     
@@ -190,6 +201,16 @@ def __addOutputOption(optionManager):
                  default=False,
                  help="Don't create an output DMS is it is not existing")
 
+    group.add_argument('--max-elts',
+                 action="store", dest="obi:maxelts",
+                 metavar='<N>',
+                 default=1000,
+                 type=int,
+                 help="Maximum number of elements per line in a column "
+                      "(e.g. the number of different keys in a dictionary-type "
+                      "key from sequence headers). If the number of different keys "
+                      "is greater than N, the values are stored as character strings")
+
 
 def addMinimalOutputOption(optionManager):
     __addOutputOption(optionManager)