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Cython API: obi import can now import ngsfilter files and tabular files

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This commit is contained in:
Celine Mercier
2018-03-12 18:10:43 +01:00
parent 8a0b95c1d6
commit 15e43bb9a1
9 changed files with 168 additions and 142 deletions
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24
python/obitools3/apps/optiongroups/__init__.py
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@ -25,8 +25,8 @@ def __addInputOption(optionManager):
group.add_argument('--na-string',
action="store", dest="obi:nastring",
default=b"NA",
type=bytes,
default="NA",
type=str,
help="String associated to Non Available (NA) values")
@ -61,7 +61,7 @@ def __addSequenceInputOption(optionManager):
action="store_const", dest="obi:format",
default=None,
const=b'ngsfilter',
help="Input file is a ngsfilter file")
help="Input file is an ngsfilter file")
group.add_argument('--ecopcr-result',
action="store_const", dest="obi:format",
@ -75,6 +75,12 @@ def __addSequenceInputOption(optionManager):
const=b'ecoprimers',
help="Input file is the result of an ecoprimers")
group.add_argument('--tabular',
action="store_const", dest="obi:format",
default=None,
const=b'tabular',
help="Input file is a tabular file")
group.add_argument('--skip-on-error',
action="store_true", dest="obi:skiperror",
default=False,
@ -120,13 +126,13 @@ def __addTabularInputOption(optionManager):
group.add_argument('--sep',
action="store", dest="obi:sep",
default=None,
type=bytes,
type=str,
help="Column separator")
group.add_argument('--dec',
action="store", dest="obi:dec",
default=b".",
type=bytes,
default=".",
type=str,
help="Decimal separator")
group.add_argument('--strip-white',
@ -141,8 +147,8 @@ def __addTabularInputOption(optionManager):
group.add_argument('--comment-char',
action="store", dest="obi:commentchar",
default=b"#",
type=bytes,
default="#",
type=str,
help="Lines starting by this char are considered as comment")
def __addTaxonomyInputOption(optionManager):
@ -171,7 +177,7 @@ def addSequenceInputOption(optionManager):
__addSequenceInputOption(optionManager)
def addTabularInputOption(optionManager):
__addInputOption(optionManager)
#__addInputOption(optionManager) # TODO discuss conflict
__addTabularInputOption(optionManager)
def addTaxonomyInputOption(optionManager):