Add a first group of options

python/obitools3/apps/optiongroups/__init__.py

@@ -0,0 +1,50 @@
+def addInputOption(optionManager):
+
+    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",
+                     metavar='<N>',
+                     default=None,
+                     type='int',
+                     help="skip the N first sequences")
+
+    group.add_argument('--only',
+                     action="store", dest="only",
+                     metavar='<N>',
+                     default=None,
+                     type='int',
+                     help="treat only N sequences")
+
+    group = optionManager.add_argument_group("Input format options",
+                    "If not specified, a test is done to determine the file format")
+
+    group.add_argument('--skip-on-error',
+                     action="store_true", dest="skiperror",
+                     default=False,
+                     help="Skip sequence entries with parse error")
+
+    group.add_argument('--quality-sanger',
+                     action="store_const", dest="seqinformat",
+                     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",
+                     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",
+                     default=None,
+                     const='nuc',
+                     help="Input file contains nucleic sequences")
+    
+    group.add_argument('--prot',
+                     action="store_const", dest="moltype",
+                     default=None,
+                     const='pep',
+                     help="Input file contains protein sequences")

python/obitools3/commands/grep.pyx

@@ -4,6 +4,8 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms.dms import DMS       # TODO cimport doesn't work
 from obitools3.dms.view.view import View, Line_selection    # TODO cimport doesn't work
  
+ 
+from obitools3.apps.optiongroups import addInputOption
 from functools import reduce
 import time
  
@@ -15,6 +17,8 @@ default_config = {   'inputview'    : None,
  
 def addOptions(parser):
     
+    addInputOption(parser)
+ 
     # TODO put this common group somewhere else but I don't know where
     group=parser.add_argument_group('DMS and view options')