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import codecs
def unescaped_str(arg_str):
return arg_str.encode('latin-1', 'backslashreplace').decode('unicode-escape')
def __addInputOption(optionManager):
optionManager.add_argument(
dest='obi:inputURI',
metavar='INPUT',
help='Data source URI')
group = optionManager.add_argument_group("Restriction to a sub-part options",
"Allows to limit analysis to a sub-part of the input")
group.add_argument('--skip',
action="store", dest="obi:skip",
metavar='<N>',
default=None,
type=int,
help="skip the N first sequences")
group.add_argument('--only',
action="store", dest="obi:only",
metavar='<N>',
default=None,
type=int,
help="treat only N sequences")
def __addImportInputOption(optionManager):
group = optionManager.add_argument_group("Input format options for imported files")
group.add_argument('--fasta-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'fasta',
help="Input file is in sanger fasta format")
group.add_argument('--fastq-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'fastq',
help="Input file is in fastq format")
group.add_argument('--silva-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'silva',
help="Input file is in SILVA fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
group.add_argument('--rdp-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'rdp',
help="Input file is in RDP training set fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
group.add_argument('--unite-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'unite',
help="Input file is in UNITE fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
group.add_argument('--sintax-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'sintax',
help="Input file is in SINTAX fasta format. If NCBI taxonomy provided with --taxonomy, taxid and scientific name will be added for each sequence.")
group.add_argument('--embl-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'embl',
help="Input file is in embl nucleic format")
group.add_argument('--genbank-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'genbank',
help="Input file is in genbank nucleic format")
group.add_argument('--ngsfilter-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'ngsfilter',
help="Input file is an ngsfilter file. If not using tags, use ':' or 'None:None' or '-:-' or any combination")
group.add_argument('--ecopcr-result-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'ecopcr',
help="Input file is the result of an ecoPCR (version 2)")
group.add_argument('--ecoprimers-result-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'ecoprimers',
help="Input file is the result of an ecoprimers")
group.add_argument('--tabular-input',
action="store_const", dest="obi:inputformat",
default=None,
const=b'tabular',
help="Input file is a tabular file")
group.add_argument('--no-skip-on-error',
action="store_false", dest="obi:skiperror",
default=True,
help="Don't skip sequence entries with parsing errors (default: they are skipped)")
group.add_argument('--no-quality',
action="store_true", dest="obi:noquality",
default=False,
help="Do not import fastQ quality")
group.add_argument('--quality-sanger',
action="store_const", dest="obi:qualityformat",
default=None,
const=b'sanger',
help="Fastq quality is encoded following sanger format (standard fastq)")
group.add_argument('--quality-solexa',
action="store_const", dest="obi:qualityformat",
default=None,
const=b'solexa',
help="Fastq quality is encoded following solexa sequencer format")
group.add_argument('--nuc',
action="store_const", dest="obi:moltype",
default=None,
const=b'nuc',
help="Input file contains nucleic sequences")
group.add_argument('--prot',
action="store_const", dest="obi:moltype",
default=None,
const=b'pep',
help="Input file contains protein sequences")
group.add_argument('--input-na-string',
action="store", dest="obi:inputnastring",
default="NA",
type=str,
help="String associated with Non Available (NA) values in the input")
def __addTabularOption(optionManager):
group = optionManager.add_argument_group("Input and output format options for tabular files")
group.add_argument('--no-header',
action="store_false", dest="obi:header",
default=True,
help="Don't print the header (first line with column names")
group.add_argument('--sep',
action="store", dest="obi:sep",
default="\t",
type=unescaped_str,
help="Column separator")
def __addTabularInputOption(optionManager):
group = optionManager.add_argument_group("Input format options for tabular files")
__addTabularOption(optionManager)
group.add_argument('--dec',
action="store", dest="obi:dec",
default=".",
type=str,
help="Decimal separator")
group.add_argument('--strip-white',
action="store_false", dest="obi:stripwhite",
default=True,
help="Remove white chars at the beginning and the end of values")
group.add_argument('--blank-line-skip',
action="store_false", dest="obi:blanklineskip",
default=True,
help="Skip empty lines")
group.add_argument('--comment-char',
action="store", dest="obi:commentchar",
default="#",
type=str,
help="Lines starting by this char are considered as comment")
def __addTabularOutputOption(optionManager):
group = optionManager.add_argument_group("Output format options for tabular files")
__addTabularOption(optionManager)
group.add_argument('--na-int-stay-na',
action="store_false", dest="obi:na_int_to_0",
help="NA (Non available) integer values should be exported as NA in tabular output (default: they are converted to 0 for tabular output).") # TODO
def __addTaxdumpInputOption(optionManager): # TODO maybe not the best way to do it
group = optionManager.add_argument_group("Input format options for taxdump")
group.add_argument('--taxdump',
action="store_true", dest="obi:taxdump",
default=False,
help="Whether the input is a taxdump")
def __addTaxonomyOption(optionManager):
group = optionManager.add_argument_group("Input format options for taxonomy")
group.add_argument('--taxonomy',
action="store", dest="obi:taxoURI",
default=None,
help="Taxonomy URI")
#TODO option bool to download taxo if URI doesn't exist
def addMinimalInputOption(optionManager):
__addInputOption(optionManager)
def addImportInputOption(optionManager):
__addInputOption(optionManager)
__addImportInputOption(optionManager)
def addTabularInputOption(optionManager):
__addTabularInputOption(optionManager)
def addTabularOutputOption(optionManager):
__addTabularOutputOption(optionManager)
def addTaxonomyOption(optionManager):
__addTaxonomyOption(optionManager)
def addTaxdumpInputOption(optionManager):
__addTaxdumpInputOption(optionManager)
def addAllInputOption(optionManager):
__addInputOption(optionManager)
__addImportInputOption(optionManager)
__addTabularInputOption(optionManager)
__addTabularOutputOption(optionManager)
__addTaxonomyOption(optionManager)
__addTaxdumpInputOption(optionManager)
def __addOutputOption(optionManager):
optionManager.add_argument(
dest='obi:outputURI',
metavar='OUTPUT',
help='Data destination URI')
def __addDMSOutputOption(optionManager):
group = optionManager.add_argument_group("Output options for DMS data")
group.add_argument('--no-create-dms',
action="store_true", dest="obi:nocreatedms",
default=False,
help="Don't create an output DMS if it does not already exist")
def __addEltLimitOption(optionManager):
group = optionManager.add_argument_group("Option to limit the number of elements per line in columns")
group.add_argument('--max-elts',
action="store", dest="obi:maxelts",
metavar='<N>',
default=1000000,
type=int,
help="Maximum number of elements per line in a column "
"(e.g. the number of different keys in a dictionary-type "
"key from sequence headers). If the number of different keys "
"is greater than N, the values are stored as character strings")
def __addExportOutputOption(optionManager):
group = optionManager.add_argument_group("Output format options for exported files")
group.add_argument('-o',
dest='obi:outputURI',
metavar='OUTPUT',
help='Data destination URI')
group.add_argument('--fasta-output',
action="store_const", dest="obi:outputformat",
default=None,
const=b'fasta',
help="Output file is in sanger fasta format")
group.add_argument('--fastq-output',
action="store_const", dest="obi:outputformat",
default=None,
const=b'fastq',
help="Output file is in fastq format")
group.add_argument('--tab-output',
action="store_const", dest="obi:outputformat",
default=None,
const=b'tabular',
help="Output file is in tabular format")
group.add_argument('--metabaR-output',
action="store_const", dest="obi:outputformat",
default=None,
const=b'metabaR',
help="Export the files needed by the obifiles_to_metabarlist function of the metabaR package")
group.add_argument('--metabaR-prefix',
action="store", dest="obi:metabarprefix",
type=str,
help="Prefix for the files when using --metabaR-output option")
group.add_argument('--metabaR-ngsfilter',
action="store", dest="obi:metabarngsfilter",
type=str,
default=None,
help="URI to the ngsfilter view when using --metabaR-output option (if not provided, it is not exported)")
group.add_argument('--metabaR-samples',
action="store", dest="obi:metabarsamples",
type=str,
default=None,
help="URI to the sample metadata view when using --metabaR-output option (if not provided, it is built as just a list of the sample names)")
group.add_argument('--only-keys',
action="append", dest="obi:only_keys",
type=str,
default=[],
help="Only export the given keys (columns).")
group.add_argument('--print-na',
action="store_true", dest="obi:printna",
default=False,
help="Print Non Available (NA) values in the output")
group.add_argument('--output-na-string',
action="store", dest="obi:outputnastring",
default="NA",
type=str,
help="String associated with Non Available (NA) values in the output")
def __addNoProgressBarOption(optionManager):
group = optionManager.add_argument_group("Option to deactivate the display of the progress bar")
group.add_argument('--no-progress-bar',
action="store_true", dest="obi:noprogressbar",
default=False,
help="Do not display progress bar")
def addMinimalOutputOption(optionManager):
__addOutputOption(optionManager)
__addDMSOutputOption(optionManager)
def addTabularOutputOption(optionManager):
__addTabularOption(optionManager)
def addExportOutputOption(optionManager):
__addExportOutputOption(optionManager)
__addTabularOutputOption(optionManager)
def addAllOutputOption(optionManager):
__addOutputOption(optionManager)
__addDMSOutputOption(optionManager)
__addExportOutputOption(optionManager)
__addTabularOutputOption(optionManager)
def addNoProgressBarOption(optionManager):
__addNoProgressBarOption(optionManager)
def addEltLimitOption(optionManager):
__addEltLimitOption(optionManager)
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