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Options stuff... ;-)

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This commit is contained in:
Eric Coissac
2017-07-25 13:07:03 +02:00
parent 28259cd88b
commit 0f6ae7dfa6
3 changed files with 22 additions and 9 deletions
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8
python/obi.py
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@ -21,9 +21,15 @@ default_config = { 'software' : "The OBITools",
'log' : False, 'log' : False,
'loglevel' : 'INFO', 'loglevel' : 'INFO',
'progress' : True, 'progress' : True,
'inputURI' : None,
'defaultdms' : None, 'defaultdms' : None,
'inputview' : None, 'inputview' : None,
'outputview' : None 'outputview' : None,
'skip' : 0,
'only' : None,
'skiperror' : True,
'qualityformat' : 'sanger',
'moltype' : 'nuc'
} }
root_config_name='obi' root_config_name='obi'

20
python/obitools3/apps/optiongroups/__init__.py
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@ -1,17 +1,23 @@
def addInputOption(optionManager): def addInputOption(optionManager):
optionManager.add_argument(
dest='obi:inputURI',
metavar='index',
help='index root filename (produced by the oa index command)')
group = optionManager.add_argument_group("Restriction to a sub-part options", group = optionManager.add_argument_group("Restriction to a sub-part options",
"Allow to limit analysis to a sub-part of the data file") "Allow to limit analysis to a sub-part of the data file")
group.add_argument('--skip', group.add_argument('--skip',
action="store", dest="skip", action="store", dest="obi:skip",
metavar='<N>', metavar='<N>',
default=None, default=None,
type='int', type='int',
help="skip the N first sequences") help="skip the N first sequences")
group.add_argument('--only', group.add_argument('--only',
action="store", dest="only", action="store", dest="obi:only",
metavar='<N>', metavar='<N>',
default=None, default=None,
type='int', type='int',
@ -21,30 +27,30 @@ def addInputOption(optionManager):
"If not specified, a test is done to determine the file format") "If not specified, a test is done to determine the file format")
group.add_argument('--skip-on-error', group.add_argument('--skip-on-error',
action="store_true", dest="skiperror", action="store_true", dest="obi:skiperror",
default=False, default=False,
help="Skip sequence entries with parse error") help="Skip sequence entries with parse error")
group.add_argument('--quality-sanger', group.add_argument('--quality-sanger',
action="store_const", dest="seqinformat", action="store_const", dest="obi:qualityformat",
default=None, default=None,
const='sanger', const='sanger',
help="Input file is in sanger fastq nucleic format (standard fastq)") help="Input file is in sanger fastq nucleic format (standard fastq)")
group.add_argument('--quality-solexa', group.add_argument('--quality-solexa',
action="store_const", dest="seqinformat", action="store_const", dest="obi:qualityformat",
default=None, default=None,
const='solexa', const='solexa',
help="Input file is in fastq nucleic format produced by solexa sequencer") help="Input file is in fastq nucleic format produced by solexa sequencer")
group.add_argument('--nuc', group.add_argument('--nuc',
action="store_const", dest="moltype", action="store_const", dest="obi:moltype",
default=None, default=None,
const='nuc', const='nuc',
help="Input file contains nucleic sequences") help="Input file contains nucleic sequences")
group.add_argument('--prot', group.add_argument('--prot',
action="store_const", dest="moltype", action="store_const", dest="obi:moltype",
default=None, default=None,
const='pep', const='pep',
help="Input file contains protein sequences") help="Input file contains protein sequences")

3
python/obitools3/commands/grep.pyx
View File

@ -12,7 +12,8 @@ import time
__title__="Grep view lines that match the given predicates" __title__="Grep view lines that match the given predicates"
default_config = { 'inputview' : None, default_config = { 'inputview' : None,
'outputview' : None 'outputview' : None,
'predicates' : []
} }
def addOptions(parser): def addOptions(parser):