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[ADD] Groups in In/Out options help display

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This commit is contained in:
Frédéric Boyer
2013-04-17 13:25:47 +00:00
parent 0f348ec4fd
commit 0288b0a7fd
2 changed files with 87 additions and 75 deletions
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60
src/obitools/format/options.py
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@ -32,6 +32,9 @@ from obitools.format.sequence import skipOnErrorIterator
from obitools import BioSequence from obitools import BioSequence
from obitools.utils import FakeFile from obitools.utils import FakeFile
def binarySequenceIterator(lineiterator): def binarySequenceIterator(lineiterator):
f = FakeFile(lineiterator) f = FakeFile(lineiterator)
@ -48,112 +51,121 @@ def binarySequenceIterator(lineiterator):
def addInputFormatOption(optionManager): def addInputFormatOption(optionManager):
optionManager.add_option('--genbank',
group = optionManager.add_option_group("Input Format Options",
"If not specified, a test is done to determine the file format")
group.add_option('--genbank',
action="store_const", dest="seqinformat", action="store_const", dest="seqinformat",
default=None, default=None,
const='genbank', const='genbank',
help="input file is in genbank format") help="input file is in genbank format")
optionManager.add_option('--embl', group.add_option('--embl',
action="store_const", dest="seqinformat", action="store_const", dest="seqinformat",
default=None, default=None,
const='embl', const='embl',
help="input file is in embl format") help="input file is in embl format")
optionManager.add_option('--skip-on-error', group.add_option('--skip-on-error',
action="store_true", dest="skiperror", action="store_true", dest="skiperror",
default=False, default=False,
help="skip sequence entries with parse error") help="skip sequence entries with parse error")
optionManager.add_option('--fasta', group.add_option('--fasta',
action="store_const", dest="seqinformat", action="store_const", dest="seqinformat",
default=None, default=None,
const='fasta', const='fasta',
help="input file is in fasta nucleic format (including obitools fasta extentions)") help="input file is in fasta nucleic format (including obitools fasta extentions)")
optionManager.add_option('--ecopcr', group.add_option('--ecopcr',
action="store_const", dest="seqinformat", action="store_const", dest="seqinformat",
default=None, default=None,
const='ecopcr', const='ecopcr',
help="input file is in ecopcr format") help="input file is in ecopcr format")
optionManager.add_option('--raw-fasta', group.add_option('--raw-fasta',
action="store_const", dest="seqinformat", action="store_const", dest="seqinformat",
default=None, default=None,
const='rawfasta', const='rawfasta',
help="input file is in fasta format (but more tolerant to format variant)") help="input file is in fasta format (but more tolerant to format variant)")
# optionManager.add_option('--fna', # group.add_option('--fna',
# action="store_const", dest="seqinformat", # action="store_const", dest="seqinformat",
# default=None, # default=None,
# const='fna', # const='fna',
# help="input file is in fasta nucleic format produced by 454 sequencer pipeline") # help="input file is in fasta nucleic format produced by 454 sequencer pipeline")
# #
# optionManager.add_option('--qual', # group.add_option('--qual',
# action="store", dest="withqualfile", # action="store", dest="withqualfile",
# type='str', # type='str',
# default=None, # default=None,
# help="Specify the name of a quality file produced by 454 sequencer pipeline") # help="Specify the name of a quality file produced by 454 sequencer pipeline")
optionManager.add_option('--sanger', group.add_option('--sanger',
action="store_const", dest="seqinformat", action="store_const", dest="seqinformat",
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)")
optionManager.add_option('--solexa', group.add_option('--solexa',
action="store_const", dest="seqinformat", action="store_const", dest="seqinformat",
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")
optionManager.add_option('--illumina', #===========================================================================
action="store_const", dest="seqinformat", # group.add_option('--illumina',
default=None, # action="store_const", dest="seqinformat",
const='illumina', # default=None,
help="input file is in fastq nucleic format produced by old solexa sequencer") # const='illumina',
# help="input file is in fastq nucleic format produced by old solexa sequencer")
#===========================================================================
optionManager.add_option('--nuc', group.add_option('--nuc',
action="store_const", dest="moltype", action="store_const", dest="moltype",
default=None, default=None,
const='nuc', const='nuc',
help="input file is nucleic sequences") help="input file is nucleic sequences")
optionManager.add_option('--prot', group.add_option('--prot',
action="store_const", dest="moltype", action="store_const", dest="moltype",
default=None, default=None,
const='pep', const='pep',
help="input file is protein sequences") help="input file is protein sequences")
def addOutputFormatOption(optionManager): def addOutputFormatOption(optionManager):
group = optionManager.add_option_group("Output Format Options")
# optionManager.add_option('-B','--bin-output', # optionManager.add_option('-B','--bin-output',
# action="store_const", dest="output", # action="store_const", dest="output",
# default=None, # default=None,
# const=dump, # const=dump,
# help="output sequences in binary format") # help="output sequences in binary format")
optionManager.add_option('--fastq-output', group.add_option('--fastq-output',
action="store_const", dest="output", action="store_const", dest="output",
default=None, default=None,
const=formatFastq, const=formatFastq,
help="output sequences in sanger fastq format") help="output sequences in sanger fastq format")
optionManager.add_option('--fasta-output', group.add_option('--fasta-output',
action="store_const", dest="output", action="store_const", dest="output",
default=None, default=None,
const=formatFasta, const=formatFasta,
help="output sequences in obitools fasta format") help="output sequences in obitools fasta format")
optionManager.add_option('--sap-output', group.add_option('--sap-output',
action="store_const", dest="output", action="store_const", dest="output",
default=None, default=None,
const=formatSAPFastaGenerator, const=formatSAPFastaGenerator,
help="output sequences in sap fasta format") help="output sequences in sap fasta format")
optionManager.add_option('--strict-sap', group.add_option('--strict-sap',
action='store_true',dest='strictsap', action='store_true',dest='strictsap',
default=False, default=False,
help="Print sequences in upper case (default is lower case)") help="Print sequences in upper case (default is lower case)")
optionManager.add_option('--ecopcrDB-output', group.add_option('--ecopcrDB-output',
action="store", dest="ecopcroutput", action="store", dest="ecopcroutput",
default=None, default=None,
help="output sequences in ecopcr database format") help="output sequences in ecopcr database format")
optionManager.add_option('--uppercase', group.add_option('--uppercase',
action='store_true',dest='uppercase', action='store_true',dest='uppercase',
default=False, default=False,
help="Print sequences in upper case (default is lower case)") help="Print sequences in upper case (default is lower case)")

2
src/obitools/options/__init__.py
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@ -7,7 +7,6 @@ import sys
from logging import debug from logging import debug
from optparse import OptionParser from optparse import OptionParser
from optparse import OptionGroup
from optparse import IndentedHelpFormatter from optparse import IndentedHelpFormatter
from obitools.utils import universalOpen from obitools.utils import universalOpen
@ -38,6 +37,7 @@ class ObiHelpFormatter (IndentedHelpFormatter):
"%*s* %s *" % (self.current_indent, "", heading), "%*s* %s *" % (self.current_indent, "", heading),
"%*s%s\n" % (self.current_indent, "", '*'*(len(heading)+4)))) "%*s%s\n" % (self.current_indent, "", '*'*(len(heading)+4))))
def getOptionManager(optionDefinitions,entryIterator=None,progdoc=None,checkFormat=False): def getOptionManager(optionDefinitions,entryIterator=None,progdoc=None,checkFormat=False):
''' '''
Build an option manager function. that is able to parse Build an option manager function. that is able to parse