Add a first group of options

2017-07-25 11:14:30 +02:00
parent 59dd0a8a8c
commit b24be84b0a
2 changed files with 54 additions and 0 deletions
--- a/python/obitools3/apps/optiongroups/init.py
+++ b/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")