Options stuff... ;-)

python/obi.py

@@ -21,9 +21,15 @@ default_config = { 'software'       : "The OBITools",
                    'log'            : False,
                    'loglevel'       : 'INFO',
                    'progress'       : True,
+                   'inputURI'       : None,
                    'defaultdms'     : None,
                    'inputview'      : None,
-                   'outputview'     : None
+                   'outputview'     : None,
+                   'skip'           : 0,
+                   'only'           : None,
+                   'skiperror'      : True,
+                   'qualityformat'  : 'sanger',
+                   'moltype'        : 'nuc'
                   }
 
 root_config_name='obi'

python/obitools3/apps/optiongroups/__init__.py

@@ -1,17 +1,23 @@
 def addInputOption(optionManager):
     
+    optionManager.add_argument(
+                    dest='obi:inputURI',  
+                    metavar='index', 
+                    help='index root filename (produced by the oa index command)')
+    
+
     group = optionManager.add_argument_group("Restriction to a sub-part options",
                     "Allow to limit analysis to a sub-part of the data file")
 
     group.add_argument('--skip',
-                     action="store", dest="skip",
+                     action="store", dest="obi:skip",
                      metavar='<N>',
                      default=None,
                      type='int',
                      help="skip the N first sequences")
 
     group.add_argument('--only',
-                     action="store", dest="only",
+                     action="store", dest="obi:only",
                      metavar='<N>',
                      default=None,
                      type='int',
@@ -21,30 +27,30 @@ def addInputOption(optionManager):
                     "If not specified, a test is done to determine the file format")
 
     group.add_argument('--skip-on-error',
-                     action="store_true", dest="skiperror",
+                     action="store_true", dest="obi:skiperror",
                      default=False,
                      help="Skip sequence entries with parse error")
 
     group.add_argument('--quality-sanger',
-                     action="store_const", dest="seqinformat",
+                     action="store_const", dest="obi:qualityformat",
                      default=None,
                      const='sanger',
                      help="Input file is in sanger fastq nucleic format (standard fastq)")
 
     group.add_argument('--quality-solexa',
-                     action="store_const", dest="seqinformat",
+                     action="store_const", dest="obi:qualityformat",
                      default=None,
                      const='solexa',
                      help="Input file is in fastq nucleic format produced by solexa sequencer")
 
     group.add_argument('--nuc',
-                     action="store_const", dest="moltype",
+                     action="store_const", dest="obi:moltype",
                      default=None,
                      const='nuc',
                      help="Input file contains nucleic sequences")
     
     group.add_argument('--prot',
-                     action="store_const", dest="moltype",
+                     action="store_const", dest="obi:moltype",
                      default=None,
                      const='pep',
                      help="Input file contains protein sequences")

python/obitools3/commands/grep.pyx

@@ -12,7 +12,8 @@ import time
 __title__="Grep view lines that match the given predicates"
  
 default_config = {   'inputview'    : None,
-                     'outputview'   : None
+                     'outputview'   : None,
+                     'predicates'   : []
                  }
  
 def addOptions(parser):