From b926ca3997235231ef8c6b2a900949546f466780 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Mon, 28 Mar 2016 15:04:06 +0200
Subject: [PATCH] A template for a command

---
 python/obitools3/commands/__init__.py |  0
 python/obitools3/commands/count.py    | 44 +++++++++++++++++++++++++++
 2 files changed, 44 insertions(+)
 create mode 100644 python/obitools3/commands/__init__.py
 create mode 100644 python/obitools3/commands/count.py

diff --git a/python/obitools3/commands/__init__.py b/python/obitools3/commands/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/python/obitools3/commands/count.py b/python/obitools3/commands/count.py
new file mode 100644
index 0000000..28bd996
--- /dev/null
+++ b/python/obitools3/commands/count.py
@@ -0,0 +1,44 @@
+'''
+Created on 8 mars 2016
+
+@author: coissac
+'''
+
+from obitools3.apps.progress import ProgressBar  # @UnresolvedImport
+import time
+
+__title__="Counts sequences in a sequence set"
+
+
+default_config = {   'countmode'       : None
+                 }
+
+def addOptions(parser):
+    parser.add_argument(dest='obi:input',     metavar='obi:input', 
+                                              nargs='?', 
+                                              default=None,
+                        help='input data set' )
+
+    group=parser.add_argument_group('Obicount specific options')
+    group.add_argument('-s','--sequence',
+                             action="store_true", dest="count:sequence",
+                             default=False,
+                             help="Prints only the number of sequence records."
+                             )
+ 
+    group.add_argument('-a','--all',
+                             action="store_true", dest="count:all",
+                             default=False,
+                             help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False)."
+                             )
+
+    
+    
+def run(config):
+    # The code of my command
+    pb = ProgressBar(1000,config,seconde=1)
+    
+    for i in range(1,1001):
+        pb(i)
+        time.sleep(0.01)
+