1st version of obi align command and reworked functions that handle

column alignment

python/obitools3/commands/align.pyx

@@ -0,0 +1,128 @@
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.obidms._obidms import OBIDMS, OBIView    # TODO cimport doesn't work
+
+
+import time
+
+__title__="Aligns one sequence column with itself or two sequence columns"
+
+
+default_config = {   'inputview'    : None,
+                     'skip'         : 0,
+                     'only'         : None,
+                     'skiperror'    : False,
+                     'moltype'      : 'nuc',
+                 }
+
+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('--input-view','-i',
+                       action="store", dest="obi:inputview",
+                       metavar='<INPUT VIEW NAME>',
+                       default=None,
+                       type=str,
+                       help="Name of the input view, either raw if the view is in the default DMS,"
+                            " or in the form 'dms:view' if it is in another DMS.")
+
+    # TODO eventually 2nd view, or 2nd column?
+
+    group.add_argument('--output-view','-o',
+                       action="store", dest="obi:outputview",
+                       metavar='<OUTPUT VIEW NAME>',
+                       default=None,
+                       type=str,
+                       help="Name of the output view, either raw if the view is in the default DMS,"
+                            " or in the form 'dms:view' if it is in another DMS.")
+
+
+    group=parser.add_argument_group('obi align specific options')
+
+    group.add_argument('--lcs','-C',
+                       action="store", dest="align:alitype",
+                       metavar='<ALIGNMENT TYPE>',
+                       default='lcs',
+                       type=str,
+                       help="Compute alignment using the LCS method.")
+ 
+    group.add_argument('--threshold','-t',
+                       action="store", dest="align:threshold",
+                       metavar='<THRESHOLD>',
+                       default=0.0,
+                       type=float,
+                       help="Score threshold. If the score is normalized and expressed in similarity (default),"
+                            " it is an identity, e.g. 0.95 for an identity of 95%%. If the score is normalized"
+                            " and expressed in distance, it is (1.0 - identity), e.g. 0.05 for an identity of 95%%."
+                            " If the score is not normalized and expressed in similarity, it is the length of the"
+                            " Longest Common Subsequence. If the score is not normalized and expressed in distance,"
+                            " it is (reference length - LCS length)."
+                            " Only sequence pairs with a similarity above <THRESHOLD> are printed. Default: 0.00"
+                            " (no threshold).")
+
+    group.add_argument('--longest_length','-L',
+                       action="store_const", dest="align:reflength",
+                       default="ali",
+                       const="longest",
+                       help="The reference length is the length of the longest sequence."
+                            " Default: the reference length is the length of the alignment.")
+
+    group.add_argument('--shortest_length','-l',
+                       action="store_const", dest="align:reflength",
+                       default="ali",
+                       const="shortest",
+                       help="The reference length is the length of the shortest sequence."
+                            " Default: the reference length is the length of the alignment.")
+
+    group.add_argument('--raw','-r',
+                       action="store_false", dest="align:normalize",
+                       default=True,
+                       help="Raw score, not normalized. Default: score is normalized with the reference sequence length.")
+
+    group.add_argument('--distance','-D',
+                       action="store_false", dest="align:similarity",
+                       default=True,
+                       help="Score is expressed in distance. Default: score is expressed in similarity.")
+
+
+    
+def run(config):
+  
+    #pb = ProgressBar(1, config, seconde=5)  # TODO
+    
+    # Open DMS
+    d = OBIDMS(config['obi']['defaultdms'])
+    
+    # Open input view 1
+    iview = d.open_view(config['obi']['inputview'])
+
+    # TODO Open input view 2 if there is one
+
+    # Create output view if necessary
+    if config['obi']['outputview'] is not None :
+        oview = d.new_view(config['obi']['outputview'])
+    else :
+        oview = None
+    
+    # TODO Take other alignment types into account when they'll be implemented
+    
+    # Call cython alignment function
+    iview.align(output_view=oview)
+     
+    print("Done.")
+    
+    
+
+    
+    
+    
+    
+