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Cython API: Added basic taxonomy option

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This commit is contained in:
Celine Mercier
2017-10-04 15:42:17 +02:00
parent ae24a807da
commit b4088a7928
1 changed files with 16 additions and 2 deletions
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18
python/obitools3/apps/optiongroups/__init__.py
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@ -144,7 +144,17 @@ def __addTabularInputOption(optionManager):
default=b"#",
type=bytes,
help="Lines starting by this char are considered as comment")
def __addTaxonomyInputOption(optionManager):
group = optionManager.add_argument_group("Input format options for taxonomy")
group.add_argument('--taxonomy',
action="store", dest="obi:taxoURI",
default=None,
help="Taxonomy URI")
#TODO option bool to download taxo if URI doesn't exist
def addMinimalInputOption(optionManager):
__addInputOption(optionManager)
@ -155,11 +165,15 @@ def addSequenceInputOption(optionManager):
def addTabularInputOption(optionManager):
__addInputOption(optionManager)
__addTabularInputOption(optionManager)
def addTaxonomyInputOption(optionManager):
__addTaxonomyInputOption(optionManager)
def addAllInputOption(optionManager):
__addInputOption(optionManager)
__addSequenceInputOption(optionManager)
__addTabularInputOption(optionManager)
__addTaxonomyInputOption(optionManager)
def __addOutputOption(optionManager):