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Cython: added possibility to output in tabular format

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This commit is contained in:
Celine Mercier
2019-03-31 15:39:38 +02:00
parent e39c1a7fbf
commit 2b8c066f8e
2 changed files with 35 additions and 7 deletions
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27
python/obitools3/apps/optiongroups/__init__.py
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@ -115,9 +115,9 @@ def __addImportInputOption(optionManager):
type=str,
help="String associated with Non Available (NA) values in the input")
def __addTabularInputOption(optionManager):
group = optionManager.add_argument_group("Input format options for tabular files")
def __addTabularOption(optionManager):
group = optionManager.add_argument_group("Input and output format options for tabular files")
group.add_argument('--header',
action="store_true", dest="obi:header",
@ -126,9 +126,15 @@ def __addTabularInputOption(optionManager):
group.add_argument('--sep',
action="store", dest="obi:sep",
default=None,
default="\t",
type=str,
help="Column separator")
def __addTabularInputOption(optionManager):
group = optionManager.add_argument_group("Input format options for tabular files")
__addTabularOption(optionManager)
group.add_argument('--dec',
action="store", dest="obi:dec",
@ -244,6 +250,12 @@ def __addExportOutputOption(optionManager):
const=b'fastq',
help="Output file is in fastq format")
group.add_argument('--tab-output',
action="store_const", dest="obi:outputformat",
default=None,
const=b'tabular',
help="Output file is in tabular format")
group.add_argument('--print-na',
action="store_true", dest="obi:printna",
default=False,
@ -260,13 +272,20 @@ def addMinimalOutputOption(optionManager):
__addOutputOption(optionManager)
__addDMSOutputOption(optionManager)
def addTabularOutputOption(optionManager):
__addTabularOption(optionManager)
def addExportOutputOption(optionManager):
__addOutputOption(optionManager)
__addExportOutputOption(optionManager)
__addTabularOption(optionManager)
def addAllOutputOption(optionManager):
__addOutputOption(optionManager)
__addDMSOutputOption(optionManager)
__addExportOutputOption(optionManager)
__addTabularOption(optionManager)