def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_path = opts.input_path
out_path = opts.out_path
output_CSS_statistics = opts.output_CSS_statistics
DESeq_negatives_to_zero = opts.DESeq_negatives_to_zero
algorithm = opts.algorithm
list_algorithms = opts.list_algorithms
if list_algorithms:
print 'Available normalization algorithms are:\n%s' % ', '.join(
algorithm_list())
else:
almost_required_options = ['input_path', 'out_path']
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if algorithm == 'CSS':
if os.path.isdir(input_path):
multiple_file_normalize_CSS(input_path, out_path,
output_CSS_statistics)
elif os.path.isfile(input_path):
normalize_CSS(input_path, out_path, output_CSS_statistics)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
elif algorithm == 'DESeq2':
if os.path.isdir(input_path):
multiple_file_normalize_DESeq2(input_path, out_path,
DESeq_negatives_to_zero)
elif os.path.isfile(input_path):
normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown normalization algorithm: %s" %
algorithm)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_path = opts.input_path
out_path = opts.out_path
output_CSS_statistics = opts.output_CSS_statistics
DESeq_negatives_to_zero = opts.DESeq_negatives_to_zero
algorithm = opts.algorithm
list_algorithms = opts.list_algorithms
if list_algorithms:
print 'Available normalization algorithms are:\n%s' % ', '.join(algorithm_list())
else:
almost_required_options = ['input_path', 'out_path']
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if algorithm == 'CSS':
if os.path.isdir(input_path):
multiple_file_normalize_CSS(input_path, out_path, output_CSS_statistics)
elif os.path.isfile(input_path):
normalize_CSS(input_path, out_path, output_CSS_statistics)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
elif algorithm == 'DESeq2':
if os.path.isdir(input_path):
multiple_file_normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero)
elif os.path.isfile(input_path):
normalize_DESeq2(input_path, out_path, DESeq_negatives_to_zero)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown normalization algorithm: %s" % algorithm)
action='store_true',
help='output CSS statistics file. This '
'will be a directory for batch processing, and a filename for '
'single file operation [default: %default]'),
make_option('-z',
'--DESeq_negatives_to_zero',
default=False,
action='store_true',
help='replace negative numbers produced by '
'the DESeq normalization technique with zeros [default: '
'%default]'),
make_option('-a',
'--algorithm',
default='CSS',
type='choice',
choices=algorithm_list(),
help='normalization algorithm to apply to input '
'BIOM table(s). [default: %default]' +
' Available options are: '
'%s' % ', '.join(algorithm_list())),
make_option('-l',
'--list_algorithms',
action='store_true',
default=False,
help='show available normalization algorithms and exit '
'[default: %default]'),
]
script_info['version'] = __version__
def main():
help='path to the input BIOM file (e.g., the output '
'from OTU picking) or directory containing input BIOM files '
'for batch processing [REQUIRED if not passing -l]'),
make_option('-o', '--out_path', type='new_path',
help='output filename for single file operation, or output '
'directory for batch processing [REQUIRED if not passing -l]'),
make_option('-s', '--output_CSS_statistics', default=False,
action='store_true', help='output CSS statistics file. This '
'will be a directory for batch processing, and a filename for '
'single file operation [default: %default]'),
make_option('-z', '--DESeq_negatives_to_zero', default=False,
action='store_true', help='replace negative numbers produced by '
'the DESeq normalization technique with zeros [default: '
'%default]'),
make_option('-a', '--algorithm', default='CSS', type='choice',
choices=algorithm_list(), help='normalization algorithm to apply to input '
'BIOM table(s). [default: %default]' + ' Available options are: '
'%s' % ', '.join(algorithm_list())),
make_option('-l', '--list_algorithms', action='store_true', default=False,
help='show available normalization algorithms and exit '
'[default: %default]'),
]
script_info['version'] = __version__
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_path = opts.input_path
out_path = opts.out_path
