obitools/obitools
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

[ADD] option groups for ecopcr related options

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

76
src/obitools/ecopcr/options.py
View File

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