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Implements #108 export integer missing values as 0 for tables by default

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This commit is contained in:
mercierc
2021-07-21 14:41:54 +12:00
parent 32345b9ec4
commit e2932b05f2
8 changed files with 64 additions and 16 deletions
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19
python/obitools3/apps/optiongroups/__init__.py
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@ -177,6 +177,16 @@ def __addTabularInputOption(optionManager):
help="Lines starting by this char are considered as comment")
def __addTabularOutputOption(optionManager):
group = optionManager.add_argument_group("Output format options for tabular files")
__addTabularOption(optionManager)
group.add_argument('--na-int-stay-na',
action="store_false", dest="obi:na_int_to_0",
help="NA (Non available) integer values should be exported as NA in tabular output (default: they are converted to 0 for tabular output).") # TODO
def __addTaxdumpInputOption(optionManager): # TODO maybe not the best way to do it
group = optionManager.add_argument_group("Input format options for taxdump")
@ -210,6 +220,10 @@ def addTabularInputOption(optionManager):
__addTabularInputOption(optionManager)
def addTabularOutputOption(optionManager):
__addTabularOutputOption(optionManager)
def addTaxonomyOption(optionManager):
__addTaxonomyOption(optionManager)
@ -222,6 +236,7 @@ def addAllInputOption(optionManager):
__addInputOption(optionManager)
__addImportInputOption(optionManager)
__addTabularInputOption(optionManager)
__addTabularOutputOption(optionManager)
__addTaxonomyOption(optionManager)
__addTaxdumpInputOption(optionManager)
@ -314,14 +329,14 @@ def addTabularOutputOption(optionManager):
def addExportOutputOption(optionManager):
__addExportOutputOption(optionManager)
__addTabularOption(optionManager)
__addTabularOutputOption(optionManager)
def addAllOutputOption(optionManager):
__addOutputOption(optionManager)
__addDMSOutputOption(optionManager)
__addExportOutputOption(optionManager)
__addTabularOption(optionManager)
__addTabularOutputOption(optionManager)
def addNoProgressBarOption(optionManager):