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