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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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160
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.utils import FakeFile
def binarySequenceIterator(lineiterator):
f = FakeFile(lineiterator)
@ -48,112 +51,121 @@ def binarySequenceIterator(lineiterator):
def addInputFormatOption(optionManager):
optionManager.add_option('--genbank',
action="store_const", dest="seqinformat",
default=None,
const='genbank',
help="input file is in genbank format")
optionManager.add_option('--embl',
action="store_const", dest="seqinformat",
default=None,
const='embl',
help="input file is in embl format")
optionManager.add_option('--skip-on-error',
action="store_true", dest="skiperror",
default=False,
help="skip sequence entries with parse error")
optionManager.add_option('--fasta',
action="store_const", dest="seqinformat",
default=None,
const='fasta',
help="input file is in fasta nucleic format (including obitools fasta extentions)")
optionManager.add_option('--ecopcr',
action="store_const", dest="seqinformat",
default=None,
const='ecopcr',
help="input file is in ecopcr format")
optionManager.add_option('--raw-fasta',
action="store_const", dest="seqinformat",
default=None,
const='rawfasta',
help="input file is in fasta format (but more tolerant to format variant)")
group = optionManager.add_option_group("Input Format Options",
"If not specified, a test is done to determine the file format")
# optionManager.add_option('--fna',
# action="store_const", dest="seqinformat",
# default=None,
# const='fna',
# help="input file is in fasta nucleic format produced by 454 sequencer pipeline")
group.add_option('--genbank',
action="store_const", dest="seqinformat",
default=None,
const='genbank',
help="input file is in genbank format")
group.add_option('--embl',
action="store_const", dest="seqinformat",
default=None,
const='embl',
help="input file is in embl format")
group.add_option('--skip-on-error',
action="store_true", dest="skiperror",
default=False,
help="skip sequence entries with parse error")
group.add_option('--fasta',
action="store_const", dest="seqinformat",
default=None,
const='fasta',
help="input file is in fasta nucleic format (including obitools fasta extentions)")
group.add_option('--ecopcr',
action="store_const", dest="seqinformat",
default=None,
const='ecopcr',
help="input file is in ecopcr format")
group.add_option('--raw-fasta',
action="store_const", dest="seqinformat",
default=None,
const='rawfasta',
help="input file is in fasta format (but more tolerant to format variant)")
# group.add_option('--fna',
# action="store_const", dest="seqinformat",
# default=None,
# const='fna',
# help="input file is in fasta nucleic format produced by 454 sequencer pipeline")
#
# optionManager.add_option('--qual',
# action="store", dest="withqualfile",
# type='str',
# default=None,
# help="Specify the name of a quality file produced by 454 sequencer pipeline")
# group.add_option('--qual',
# action="store", dest="withqualfile",
# type='str',
# default=None,
# help="Specify the name of a quality file produced by 454 sequencer pipeline")
optionManager.add_option('--sanger',
action="store_const", dest="seqinformat",
default=None,
const='sanger',
help="input file is in sanger fastq nucleic format (standard fastq)")
group.add_option('--sanger',
action="store_const", dest="seqinformat",
default=None,
const='sanger',
help="input file is in sanger fastq nucleic format (standard fastq)")
optionManager.add_option('--solexa',
action="store_const", dest="seqinformat",
default=None,
const='solexa',
help="input file is in fastq nucleic format produced by solexa sequencer")
group.add_option('--solexa',
action="store_const", dest="seqinformat",
default=None,
const='solexa',
help="input file is in fastq nucleic format produced by solexa sequencer")
optionManager.add_option('--illumina',
action="store_const", dest="seqinformat",
default=None,
const='illumina',
help="input file is in fastq nucleic format produced by old solexa sequencer")
#===========================================================================
# group.add_option('--illumina',
# action="store_const", dest="seqinformat",
# default=None,
# const='illumina',
# help="input file is in fastq nucleic format produced by old solexa sequencer")
#===========================================================================
optionManager.add_option('--nuc',
action="store_const", dest="moltype",
default=None,
const='nuc',
help="input file is nucleic sequences")
optionManager.add_option('--prot',
action="store_const", dest="moltype",
default=None,
const='pep',
help="input file is protein sequences")
group.add_option('--nuc',
action="store_const", dest="moltype",
default=None,
const='nuc',
help="input file is nucleic sequences")
group.add_option('--prot',
action="store_const", dest="moltype",
default=None,
const='pep',
help="input file is protein sequences")
def addOutputFormatOption(optionManager):
group = optionManager.add_option_group("Output Format Options")
# optionManager.add_option('-B','--bin-output',
# action="store_const", dest="output",
# default=None,
# const=dump,
# help="output sequences in binary format")
optionManager.add_option('--fastq-output',
group.add_option('--fastq-output',
action="store_const", dest="output",
default=None,
const=formatFastq,
help="output sequences in sanger fastq format")
optionManager.add_option('--fasta-output',
group.add_option('--fasta-output',
action="store_const", dest="output",
default=None,
const=formatFasta,
help="output sequences in obitools fasta format")
optionManager.add_option('--sap-output',
group.add_option('--sap-output',
action="store_const", dest="output",
default=None,
const=formatSAPFastaGenerator,
help="output sequences in sap fasta format")
optionManager.add_option('--strict-sap',
group.add_option('--strict-sap',
action='store_true',dest='strictsap',
default=False,
help="Print sequences in upper case (default is lower case)")
optionManager.add_option('--ecopcrDB-output',
group.add_option('--ecopcrDB-output',
action="store", dest="ecopcroutput",
default=None,
help="output sequences in ecopcr database format")
optionManager.add_option('--uppercase',
group.add_option('--uppercase',
action='store_true',dest='uppercase',
default=False,
help="Print sequences in upper case (default is lower case)")

2
src/obitools/options/__init__.py
View File

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