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[ADD] option groups for ecopcr related options

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This commit is contained in:
Frédéric Boyer
2013-04-17 13:59:18 +00:00
parent e200bf60a2
commit 50ae4ef117
1 changed files with 40 additions and 36 deletions
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14
src/obitools/ecopcr/options.py
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@ -16,13 +16,15 @@ except ImportError:
def addTaxonomyDBOptions(optionManager): def addTaxonomyDBOptions(optionManager):
# addEcoBarcodeDBOption(optionManager) # addEcoBarcodeDBOption(optionManager)
optionManager.add_option('-d','--database',
group = optionManager.add_option_group('Taxonomy loading options')
group.add_option('-d','--database',
action="store", dest="taxonomy", action="store", dest="taxonomy",
metavar="<FILENAME>", metavar="<FILENAME>",
type="string", type="string",
help="ecoPCR taxonomy Database " help="ecoPCR taxonomy Database "
"name") "name")
optionManager.add_option('-t','--taxonomy-dump', group.add_option('-t','--taxonomy-dump',
action="store", dest="taxdump", action="store", dest="taxdump",
metavar="<FILENAME>", metavar="<FILENAME>",
type="string", type="string",
@ -32,7 +34,9 @@ def addTaxonomyDBOptions(optionManager):
def addTaxonomyFilterOptions(optionManager): def addTaxonomyFilterOptions(optionManager):
addTaxonomyDBOptions(optionManager) addTaxonomyDBOptions(optionManager)
optionManager.add_option('--require-rank', group = optionManager.add_option_group('Taxonomy-related selection options')
group.add_option('--require-rank',
action="append", action="append",
dest='requiredRank', dest='requiredRank',
metavar="<RANK_NAME>", metavar="<RANK_NAME>",
@ -41,7 +45,7 @@ def addTaxonomyFilterOptions(optionManager):
help="select sequence with taxid tag containing " help="select sequence with taxid tag containing "
"a parent of rank <RANK_NAME>") "a parent of rank <RANK_NAME>")
optionManager.add_option('-r','--required', group.add_option('-r','--required',
action="append", action="append",
dest='required', dest='required',
metavar="<TAXID>", metavar="<TAXID>",
@ -52,7 +56,7 @@ def addTaxonomyFilterOptions(optionManager):
"(with \n'-r taxid1 -r taxid2'), the sequences " "(with \n'-r taxid1 -r taxid2'), the sequences "
"having at least one of them are selected") "having at least one of them are selected")
optionManager.add_option('-i','--ignore', group.add_option('-i','--ignore',
action="append", action="append",
dest='ignored', dest='ignored',
metavar="<TAXID>", metavar="<TAXID>",