micca-rarefyΒΆ

Rarefies an OTU table with a depth of perc % of the least abundant sample.

$ micca-rarefy --help
usage: micca-rarefy [-h] [-v] [-p PERC] [-s SEED] input output

micca-rarefy rarefies an OTU table with a depth of perc % of the least
abundant sample.

positional arguments:
  input                 input OTU table file
  output                output OTU table file

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -p PERC, --perc PERC  depth in terms of {'const': None, 'help': 'depth in
                        terms of %reads of the least abundant sample (default
                        %(default)s)', 'option_strings': ['-p', '--perc'],
                        'dest': 'perc', 'required': False, 'nargs': None,
                        'choices': None, 'default': 80, 'prog': 'micca-
                        rarefy', 'container': <argparse._ArgumentGroup object
                        at 0x10326af10>, 'type': 'int', 'metavar': 'PERC'}eads
                        of the least abundant sample (default 80)
  -s SEED, --seed SEED  random seed for the random generator (default 0)

Example:

 $ micca-rarefy otu_table.txt rarefied.txt -p 95

micca v. 0.1.
Author: Davide Albanese <davide.albanese@fmach.it>
Fondazione Edmund Mach, 2014.

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