minor comments and changes

python/obitools3/commands/check.pyx

@@ -30,16 +30,6 @@ def addOptions(parser):
                        default=None,
                        type=str,
                        help="Name of the view.")
-  
- 
-#    group=parser.add_argument_group('obi check specific options')
- 
-#     group.add_argument('--print',
-#                      action="store", dest="less:print",
-#                      metavar='<N>',
-#                      default=None,
-#                      type=int,
-#                      help="Print N sequences (default: 10)")
  
      
 def run(config):
@@ -48,9 +38,9 @@ def run(config):
     d = DMS.open(config['obi']['defaultdms'])
      
     # Open input view uif there is one 
-    if config['obi']['inputview'] is not None :
-        iview = View.open(d, config['obi']['view'])
-        print(repr(iview))
+    if 'view' in config['obi'] :
+        view = View.open(d, config['obi']['view'])
+        print(repr(view))
     
     else :
         for v in d :

python/obitools3/commands/count.py

@@ -1,3 +1,5 @@
+#cython: language_level=3
+
 '''
 Created on 8 mars 2016
 

python/obitools3/commands/export.pyx

@@ -1,32 +1,29 @@
 # from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 # from obitools3.dms.dms import OBIDMS       # TODO cimport doesn't work
 # from obitools3.utils cimport bytes2str
-# 
+#  
 # import time
 # import re
-
-
-def run(config):
-    pass
-
+# 
+# 
 # __title__="Export a NUC_SEQS view to a fasta or fastq file"
-# 
-# 
+#  
+#  
 # 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('--input-view','-i',
 #                        action="store", dest="obi:inputview",
 #                        metavar='<INPUT VIEW NAME>',
@@ -34,76 +31,77 @@ def run(config):
 #                        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.")
-# 
+#  
 #     group=parser.add_argument_group('obi export specific options')
-# 
+#  
 #     group.add_argument('--format','-f',
 #                        action="store", dest="export:format",
 #                        metavar='<FORMAT>',
 #                        default="fasta",
 #                        type=str,
 #                        help="Export in the format <FORMAT>, 'fasta' or 'fastq'. Default: 'fasta'.")         # TODO export in csv
-# 
-# def run(config):
-#     
+#  
+def run(config):
+    pass
+#      
 #     # TODO import doesn't work
 #     NUC_SEQUENCE_COLUMN = "NUC_SEQ"
 #     ID_COLUMN = "ID"
 #     DEFINITION_COLUMN = "DEFINITION"
 #     QUALITY_COLUMN = "QUALITY"    
-#     
+#      
 #     special_columns = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
-#     
+#      
 #     # Open DMS
 #     d = OBIDMS(config['obi']['defaultdms'])
-#     
+#      
 #     # Open input view
 #     iview = d.open_view(config['obi']['inputview'])
-#     
+#      
 #     print(iview.type)
-#     
+#      
 #     # TODO check that the view has the type NUC_SEQS
 #     if ((config['export']['format'] == "fasta") or (config['export']['format'] == "fastq")) and (iview.type != "NUC_SEQS_VIEW") :   # TODO find a way to import those macros
 #         raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
-#     
+#      
 #     # Initialize the progress bar
 #     pb = ProgressBar(len(iview), config, seconde=5)
-#     
+#      
 #     i=0
 #     for seq in iview :
 #         pb(i)
-#         
+#          
 #         toprint = ">"+seq.id+" "
-#         
+#          
 #         for col_name in seq :
 #             if col_name not in special_columns :
 #                 toprint = toprint + col_name + "=" + str(seq[col_name]) + "; "
-#         
+#          
 #         if DEFINITION_COLUMN in seq :
 #             toprint = toprint + seq.definition
-#         
+#          
 #         nucseq = bytes2str(seq.nuc_seq)
-#         
+#          
 #         if config['export']['format'] == "fasta" :
 #             nucseq = re.sub("(.{60})", "\\1\n", nucseq, 0, re.DOTALL)
-#         
+#          
 #         toprint = toprint + "\n" + nucseq
-#         
+#          
 #         if config['export']['format'] == "fastq" :
 #             toprint = toprint + "\n" + "+" + "\n" + seq.get_str_quality()
-#             
+#              
 #         print(toprint)
 #         i+=1
-#         
+#          
 #     iview.close()
 #     d.close()
-#     
+#      
 #     print("Done.")
-#     
-#     
-# 
-#     
-#     
-#     
-#     
-#         
+#      
+#      
+#  
+#      
+#      
+#      
+#      
+#          

python/obitools3/commands/import.pyx

@@ -20,10 +20,6 @@ from obitools3.dms.capi.obitypes cimport obitype_t, \
 
 from obitools3.dms.capi.obierrno cimport obi_errno
 
-import time
-
-import pickle
-
 
 __title__="Imports sequences from different formats into a DMS"