New command: obi cat to concatenate views (not optimized yet)

python/obitools3/commands/cat.pyx

@@ -0,0 +1,104 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+from obitools3.utils cimport str2bytes
+from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
+from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
+from obitools3.commands.ngsfilter import REVERSE_QUALITY_COLUMN_NAME  # TODO should be stored in C
+
+import time
+import sys
+ 
+from cpython.exc cimport PyErr_CheckSignals
+
+
+__title__="Concatenate views."
+
+ 
+def addOptions(parser):
+    
+    addMinimalOutputOption(parser)
+
+    group=parser.add_argument_group('obi cat specific options')
+
+    group.add_argument("-c",
+                       action="append", dest="cat:views_to_cat",
+                       metavar="<VIEW_NAME>",
+                       default=[],
+                       type=str,
+                       help="URI of a view to concatenate. (e.g. 'my_dms/my_view'). "
+                            "Several -c options can be used on the same "
+                            "command line.")
+
+     
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi cat")
+
+    # Open the views to concatenate
+    iview_list = []
+    idms_list = []
+    total_len = 0
+    v_type = View_NUC_SEQS
+    for v_uri in config["cat"]["views_to_cat"]:
+        input = open_uri(v_uri)
+        if input is None:
+            raise Exception("Could not read input view")
+        i_dms = input[0]
+        i_view = input[1]
+        if input[2] != View_NUC_SEQS:  # Check view type (output view is nuc_seqs view if all input view are nuc_seqs view)
+            v_type = View
+        total_len += len(i_view)
+        iview_list.append(i_view)
+        idms_list.append(i_dms)
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False, 
+                      newviewtype=v_type)
+    if output is None:
+        raise Exception("Could not create output view")
+    o_dms = output[0]
+    o_view = output[1]
+    
+    # Initialize the progress bar
+    pb = ProgressBar(total_len, config, seconde=5)
+    
+    i = 0
+    for v in iview_list:
+        for l in v:
+            PyErr_CheckSignals()
+            pb(i)
+            o_view[i] = l
+            i+=1
+
+    # Deletes quality columns if there are any
+    if QUALITY_COLUMN in o_view:
+        o_view.delete_column(QUALITY_COLUMN)
+    if REVERSE_QUALITY_COLUMN_NAME in o_view:
+        o_view.delete_column(REVERSE_QUALITY_COLUMN_NAME)
+
+    pb(i, force=True)
+    print("", file=sys.stderr)
+    
+    # Save command config in DMS comments
+    command_line = " ".join(sys.argv[1:])
+    o_view.write_config(config, "cat", command_line, input_dms_name=[d.name for d in idms_list], input_view_name=[v.name for v in iview_list])
+    o_dms.record_command_line(command_line)
+
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
+    #print(repr(view), file=sys.stderr)
+
+    for d in idms_list:
+        d.close()
+    o_dms.close()
+    
+    logger("info", "Done.")