Complete the input option group functions

python/obitools3/apps/optiongroups/__init__.py

@@ -1,4 +1,4 @@
-def addInputOption(optionManager):
+def __addInputOption(optionManager):
     
     optionManager.add_argument(
                     dest='obi:inputURI',  
@@ -23,34 +23,141 @@ def addInputOption(optionManager):
                      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")
+
+
+def __addSequenceInputOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for sequence files")
+
+    group.add_argument('--fasta',
+                     action="store_const", dest="obi:format",
+                     default=None,
+                     const=b'fasta',
+                     help="Input file is in sanger fasta format")
+
+    group.add_argument('--fastq',
+                     action="store_const", dest="obi:format",
+                     default=None,
+                     const=b'fastq',
+                     help="Input file is in fastq format")
+
+    group.add_argument('--embl',
+                     action="store_const", dest="obi:format",
+                     default=None,
+                     const=b'embl',
+                     help="Input file is in embl nucleic format")
+
+    group.add_argument('--genbank',
+                     action="store_const", dest="obi:format",
+                     default=None,
+                     const=b'genbank',
+                     help="Input file is in genbank nucleic format")
+
+    group.add_argument('--ngsfilter',
+                     action="store_const", dest="obi:format",
+                     default=None,
+                     const=b'ngsfilter',
+                     help="Input file is a ngsfilter file")
+
+    group.add_argument('--ecopcr-result',
+                     action="store_const", dest="obi:format",
+                     default=None,
+                     const=b'ecopcr',
+                     help="Input file is the result of an ecoPCR (version 2)")
+
+    group.add_argument('--ecoprimers-result',
+                     action="store_const", dest="obi:format",
+                     default=None,
+                     const=b'ecoprimers',
+                     help="Input file is the result of an ecoprimers")
 
     group.add_argument('--skip-on-error',
                      action="store_true", dest="obi:skiperror",
                      default=False,
                      help="Skip sequence entries with parse error")
 
+    group.add_argument('--no-quality',
+                     action="store_true", dest="obi:noquality",
+                     default=False,
+                     help="Do not import fastQ quality")
+
     group.add_argument('--quality-sanger',
                      action="store_const", dest="obi:qualityformat",
                      default=None,
-                     const='sanger',
-                     help="Input file is in sanger fastq nucleic format (standard fastq)")
+                     const=b'sanger',
+                     help="Fastq quality is encoded following sanger format (standard fastq)")
 
     group.add_argument('--quality-solexa',
                      action="store_const", dest="obi:qualityformat",
                      default=None,
-                     const='solexa',
-                     help="Input file is in fastq nucleic format produced by solexa sequencer")
+                     const=b'solexa',
+                     help="Fastq quality is encoded following solexa sequencer format")
 
     group.add_argument('--nuc',
                      action="store_const", dest="obi:moltype",
                      default=None,
-                     const='nuc',
+                     const=b'nuc',
                      help="Input file contains nucleic sequences")
     
     group.add_argument('--prot',
                      action="store_const", dest="obi:moltype",
                      default=None,
-                     const='pep',
+                     const=b'pep',
                      help="Input file contains protein sequences")
+  
+def __addTabularInputOption(optionManager):
+    group = optionManager.add_argument_group("Input format options for tabular files")
+
+    group.add_argument('--header',
+                     action="store_true", dest="obi:header",
+                     default=False,
+                     help="First line of tabular file contains column names")
+
+    group.add_argument('--sep',
+                     action="store", dest="obi:sep",
+                     default=None,
+                     type="bytes",
+                     help="Column separator")
+    
+    group.add_argument('--dec',
+                     action="store", dest="obi:dec",
+                     default=b".",
+                     type="bytes",
+                     help="Decimal separator")
+    
+    group.add_argument('--na-string',
+                     action="store", dest="obi:nastring",
+                     default=b"NA",
+                     type="bytes",
+                     help="String associated to Non Available (NA) values")
+    
+    group.add_argument('--strip-white',
+                     action="store_false", dest="obi:stripwhite",
+                     default=True,
+                     help="Remove white chars at the beginning and the end of values")
+
+    group.add_argument('--blank-line-skip',
+                     action="store_false", dest="obi:blanklineskip",
+                     default=True,
+                     help="Skip empty lines")
+
+    group.add_argument('--comment-char',
+                     action="store", dest="obi:commentchar",
+                     default=b"#",
+                     type="bytes",
+                     help="Lines starting by this char are considered as comment")
+  
+def addMinimalOption(optionManager):
+    __addInputOption(optionManager)
+    
+def addSequenceInputOption(optionManager):
+    __addInputOption(optionManager)
+    __addSequenceInputOption(optionManager)
+    
+def addTabularInputOption(optionManager):
+    __addInputOption(optionManager)
+    __addTabularInputOption(optionManager)
+    
+def addAllInputOption(optionManager):
+    __addInputOption(optionManager)
+    __addSequenceInputOption(optionManager)
+    __addTabularInputOption(optionManager)