Added atexit command to obi import, obi uniq and obi less

python/obitools3/commands/import.pyx

@@ -12,6 +12,7 @@ from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.column.column cimport Column
 from obitools3.dms.obiseq cimport Nuc_Seq
+from obitools3.dms import DMS
 
 from obitools3.utils cimport tobytes, \
                              get_obitype, \
@@ -82,6 +83,7 @@ def run(config):
     cdef   bytes       NA_value
     global             obi_errno
         
+    DMS.obi_atexit()
     
     logger("info","obi import : imports file into an DMS")
     
@@ -238,6 +240,6 @@ def run(config):
     print("\n")
     print(view.__repr__())
   
-    input[0].close()    # TODO
+    input[0].close()    # TODO ?
     output[0].close()
 

python/obitools3/commands/less.pyx

@@ -2,6 +2,7 @@
 
 from obitools3.apps.optiongroups import addSequenceInputOption
 from obitools3.uri.decode import open_uri
+from obitools3.dms import DMS
 
  
 __title__="Less equivalent"
@@ -25,7 +26,9 @@ def run(config):
     
     cdef object entries
     cdef int    n
-
+    
+    DMS.obi_atexit()
+    
     input = open_uri(config['obi']['inputURI'])
        
     entries = input[1]

python/obitools3/commands/uniq.pyx

@@ -1,7 +1,7 @@
 #cython: language_level=3
 
 from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
-from obitools3.dms.dms cimport DMS
+from obitools3.dms import DMS
 from obitools3.dms.view.view cimport View, Line
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.column.column cimport Column, Column_line
@@ -44,6 +44,7 @@ def addOptions(parser):
                              "used to group sequences before dereplication "
                              "(option can be used several times).")
 
+# TODO discuss
 #     group.add_argument('--prefix', '-p',
 #                         action="store_true", dest="uniq:prefix",
 #                         default=False,
@@ -400,7 +401,6 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li
         merge_taxonomy_classification(o_view, taxonomy)
 
 
-     
 def run(config):
     
     cdef tuple         input
@@ -410,14 +410,16 @@ def run(config):
     cdef View_NUC_SEQS entries
     cdef View_NUC_SEQS o_view
     cdef ProgressBar   pb
-     
+    
+    DMS.obi_atexit()
+    
     logger("info","obi uniq")
     
     input = open_uri(config['obi']['inputURI'])
     
     if input[2] != View_NUC_SEQS:
         raise NotImplementedError('obi uniq only works on NUC_SEQS views')
-        
+    
     output = open_uri(config['obi']['outputURI'],
                       input=False,
                       newviewtype=View_NUC_SEQS)
@@ -434,14 +436,8 @@ def run(config):
 
     # Initialize the progress bar
     pb = ProgressBar(len(entries), config, seconde=5)
-
-# TODO
-#    if options.prefix:
-#        usm = uniqPrefixSequence
-#    else:
-    usm = uniq_sequences
         
-    usm(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'])       
+    uniq_sequences(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories'])       
 
     print("\n")
     print(repr(o_view))