From d252131950a3c680ac8b494cad4efe6653a22580 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 5 Jul 2017 13:44:12 +0200
Subject: [PATCH] Basic obi less command

---
 python/obitools3/commands/less.pyx | 57 ++++++++++++++++++++++++++++++
 1 file changed, 57 insertions(+)
 create mode 100644 python/obitools3/commands/less.pyx

diff --git a/python/obitools3/commands/less.pyx b/python/obitools3/commands/less.pyx
new file mode 100644
index 0000000..175b814
--- /dev/null
+++ b/python/obitools3/commands/less.pyx
@@ -0,0 +1,57 @@
+#cython: language_level=3
+
+from obitools3.dms.dms import DMS       # TODO cimport doesn't work
+from obitools3.dms.view.view import View    # TODO cimport doesn't work
+
+
+# TODO with URIs
+ 
+__title__="Less equivalent"
+ 
+default_config = {   'inputview'    : None,
+                 }
+ 
+def addOptions(parser):
+ 
+    # TODO put this common group somewhere else but I don't know where
+    group=parser.add_argument_group('DMS and view options')
+ 
+    group.add_argument('--default-dms','-d', 
+                       action="store", dest="obi:defaultdms",
+                       metavar='<DMS NAME>',
+                       default=None,
+                       type=str,
+                       help="Name of the default DMS for reading and writing data.")
+ 
+    group.add_argument('--view','-v',
+                       action="store", dest="obi:view",
+                       metavar='<VIEW NAME>',
+                       default=None,
+                       type=str,
+                       help="Name of the view to print.")
+  
+ 
+    group=parser.add_argument_group('obi less specific options')
+ 
+    group.add_argument('--print', '-n',
+                     action="store", dest="less:print",
+                     metavar='<N>',
+                     default=10,
+                     type=int,
+                     help="Print N sequences (default: 10)")
+ 
+
+def run(config):
+     
+    # Open DMS
+    d = DMS.open(config['obi']['defaultdms'])
+     
+    # Open input view
+    iview = View.open(d, config['obi']['inputview'])
+              
+    # Print
+    for i in range(config['less']['print']) :
+        print(repr(iview[i]))
+     
+    d.close()
+