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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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76
src/obitools/ecopcr/options.py
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@ -16,49 +16,53 @@ except ImportError:
def addTaxonomyDBOptions(optionManager):
# addEcoBarcodeDBOption(optionManager)
optionManager.add_option('-d','--database',
action="store", dest="taxonomy",
metavar="<FILENAME>",
type="string",
help="ecoPCR taxonomy Database "
"name")
optionManager.add_option('-t','--taxonomy-dump',
action="store", dest="taxdump",
metavar="<FILENAME>",
type="string",
help="NCBI Taxonomy dump repository "
group = optionManager.add_option_group('Taxonomy loading options')
group.add_option('-d','--database',
action="store", dest="taxonomy",
metavar="<FILENAME>",
type="string",
help="ecoPCR taxonomy Database "
"name")
group.add_option('-t','--taxonomy-dump',
action="store", dest="taxdump",
metavar="<FILENAME>",
type="string",
help="NCBI Taxonomy dump repository "
"name")
def addTaxonomyFilterOptions(optionManager):
addTaxonomyDBOptions(optionManager)
optionManager.add_option('--require-rank',
action="append",
dest='requiredRank',
metavar="<RANK_NAME>",
type="string",
default=[],
help="select sequence with taxid tag containing "
"a parent of rank <RANK_NAME>")
group = optionManager.add_option_group('Taxonomy-related selection options')
group.add_option('--require-rank',
action="append",
dest='requiredRank',
metavar="<RANK_NAME>",
type="string",
default=[],
help="select sequence with taxid tag containing "
"a parent of rank <RANK_NAME>")
optionManager.add_option('-r','--required',
action="append",
dest='required',
metavar="<TAXID>",
type="int",
default=[],
help="Select the sequences having "
"the ancestor of taxid <TAXID>. If several ancestors are specified "
"(with \n'-r taxid1 -r taxid2'), the sequences "
"having at least one of them are selected")
group.add_option('-r','--required',
action="append",
dest='required',
metavar="<TAXID>",
type="int",
default=[],
help="Select the sequences having "
"the ancestor of taxid <TAXID>. If several ancestors are specified "
"(with \n'-r taxid1 -r taxid2'), the sequences "
"having at least one of them are selected")
optionManager.add_option('-i','--ignore',
action="append",
dest='ignored',
metavar="<TAXID>",
type="int",
default=[],
help="ignored taxid")
group.add_option('-i','--ignore',
action="append",
dest='ignored',
metavar="<TAXID>",
type="int",
default=[],
help="ignored taxid")
def loadTaxonomyDatabase(options):