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Cython: added an option for input taxdump and and an option for the

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maximum number of elements in columns with multiple elements per line
This commit is contained in:
Celine Mercier
2017-12-13 22:25:15 +01:00
parent ea73047fc7
commit b93b982a18
1 changed files with 23 additions and 2 deletions
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25
python/obitools3/apps/optiongroups/__init__.py
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@ -154,7 +154,15 @@ def __addTaxonomyInputOption(optionManager):
help="Taxonomy URI") help="Taxonomy URI")
#TODO option bool to download taxo if URI doesn't exist #TODO option bool to download taxo if URI doesn't exist
def __addTaxdumpInputOption(optionManager):
group = optionManager.add_argument_group("Input format options for taxdump")
group.add_argument('--taxdump',
action="store", dest="obi:taxdump",
default=None,
help="Taxdump path")
def addMinimalInputOption(optionManager): def addMinimalInputOption(optionManager):
__addInputOption(optionManager) __addInputOption(optionManager)
@ -169,12 +177,15 @@ def addTabularInputOption(optionManager):
def addTaxonomyInputOption(optionManager): def addTaxonomyInputOption(optionManager):
__addTaxonomyInputOption(optionManager) __addTaxonomyInputOption(optionManager)
def addTaxdumpInputOption(optionManager):
__addTaxdumpInputOption(optionManager)
def addAllInputOption(optionManager): def addAllInputOption(optionManager):
__addInputOption(optionManager) __addInputOption(optionManager)
__addSequenceInputOption(optionManager) __addSequenceInputOption(optionManager)
__addTabularInputOption(optionManager) __addTabularInputOption(optionManager)
__addTaxonomyInputOption(optionManager) __addTaxonomyInputOption(optionManager)
__addTaxdumpInputOption(optionManager)
def __addOutputOption(optionManager): def __addOutputOption(optionManager):
@ -190,6 +201,16 @@ def __addOutputOption(optionManager):
default=False, default=False,
help="Don't create an output DMS is it is not existing") help="Don't create an output DMS is it is not existing")
group.add_argument('--max-elts',
action="store", dest="obi:maxelts",
metavar='<N>',
default=1000,
type=int,
help="Maximum number of elements per line in a column "
"(e.g. the number of different keys in a dictionary-type "
"key from sequence headers). If the number of different keys "
"is greater than N, the values are stored as character strings")
def addMinimalOutputOption(optionManager): def addMinimalOutputOption(optionManager):
__addOutputOption(optionManager) __addOutputOption(optionManager)