Obi count command

python/obitools3/commands/count.py

@@ -1,46 +0,0 @@
-#cython: language_level=3
-
-'''
-Created on 8 mars 2016
-
-@author: coissac
-'''
-
-from obitools3.apps.progress import ProgressBar  # @UnresolvedImport
-import time
-
-__title__="Counts sequences in a sequence set"
-
-
-default_config = {   'countmode'       : None
-                 }
-
-def addOptions(parser):
-    parser.add_argument(dest='obi:input',     metavar='obi:input', 
-                                              nargs='?', 
-                                              default=None,
-                        help='input data set' )
-
-    group=parser.add_argument_group('Obicount specific options')
-    group.add_argument('-s','--sequence',
-                             action="store_true", dest="count:sequence",
-                             default=False,
-                             help="Prints only the number of sequence records."
-                             )
- 
-    group.add_argument('-a','--all',
-                             action="store_true", dest="count:all",
-                             default=False,
-                             help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False)."
-                             )
-
-    
-    
-def run(config):
-    # The code of my command
-    pb = ProgressBar(1000,config,seconde=1)
-    
-    for i in range(1,1001):
-        pb(i)
-        time.sleep(0.01)
-        

python/obitools3/commands/count.pyx

@@ -0,0 +1,55 @@
+#cython: language_level=3
+
+
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.dms import DMS
+from obitools3.apps.optiongroups import addSequenceInputOption
+from obitools3.dms.capi.obiview cimport COUNT_COLUMN
+
+
+__title__="Counts sequence records"
+
+ 
+def addOptions(parser):
+ 
+    addSequenceInputOption(parser)
+ 
+    group = parser.add_argument_group('obi count specific options')
+ 
+    group.add_argument('-s','--sequence',
+                        action="store_true", dest="count:sequence",
+                        default=False,
+                        help="Prints only the number of sequence records.")
+ 
+    group.add_argument('-a','--all',
+                        action="store_true", dest="count:all",
+                        default=False,
+                        help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False).")
+
+    
+def run(config):
+    
+    DMS.obi_atexit()
+    
+    logger("info", "obi count")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input")
+    entries = input[1]
+
+    count1 = len(entries)
+    count2 = 0
+    
+    if COUNT_COLUMN in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
+        for e in entries:
+            count2+=e[COUNT_COLUMN]
+
+    if COUNT_COLUMN in entries and (config['count']['sequence'] == config['count']['all']):
+        print(count1,count2)
+    elif COUNT_COLUMN in entries and config['count']['all']:
+        print(count2)
+    else:
+        print(count1)