def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_path = opts.input_path
out_path = opts.out_path
algorithm = opts.algorithm
mapping_fp = opts.mapping_file_path
mapping_category = opts.mapping_file_category
subcategory_1 = opts.mapping_file_subcategory_1
subcategory_2 = opts.mapping_file_subcategory_2
list_algorithms = opts.list_algorithms
DESeq2_diagnostic_plots = opts.DESeq2_diagnostic_plots
if list_algorithms:
print 'Available differential abundance algorithms are:\n%s' % ', '.join(
algorithm_list())
else:
almost_required_options = [
'input_path', 'out_path', 'mapping_file_path',
'mapping_file_category', 'mapping_file_subcategory_1',
'mapping_file_subcategory_2'
]
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if algorithm == 'metagenomeSeq_fitZIG':
if os.path.isdir(input_path):
multiple_file_DA_fitZIG(input_path, out_path, mapping_fp,
mapping_category, subcategory_1,
subcategory_2)
elif os.path.isfile(input_path):
DA_fitZIG(input_path, out_path, mapping_fp, mapping_category,
subcategory_1, subcategory_2)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
elif algorithm == 'DESeq2_nbinom':
if os.path.isdir(input_path):
multiple_file_DA_DESeq2(input_path, out_path, mapping_fp,
mapping_category, subcategory_1,
subcategory_2, DESeq2_diagnostic_plots)
elif os.path.isfile(input_path):
DA_DESeq2(input_path, out_path, mapping_fp, mapping_category,
subcategory_1, subcategory_2,
DESeq2_diagnostic_plots)
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
algorithm = opts.algorithm
mapping_fp = opts.mapping_file_path
mapping_category = opts.mapping_file_category
subcategory_1 = opts.mapping_file_subcategory_1
subcategory_2 = opts.mapping_file_subcategory_2
list_algorithms = opts.list_algorithms
DESeq2_diagnostic_plots = opts.DESeq2_diagnostic_plots
if list_algorithms:
print 'Available differential abundance algorithms are:\n%s' % ', '.join(algorithm_list())
else:
almost_required_options = ['input_path', 'out_path', 'mapping_file_path', 'mapping_file_category', 'mapping_file_subcategory_1', 'mapping_file_subcategory_2']
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if algorithm == 'metagenomeSeq_fitZIG':
if os.path.isdir(input_path):
multiple_file_DA_fitZIG(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2)
elif os.path.isfile(input_path):
DA_fitZIG(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2)
else:
# it shouldn't be possible to get here
option_parser.error("Unknown input type: %s" % input_path)
elif algorithm == 'DESeq2_nbinom':
if os.path.isdir(input_path):
multiple_file_DA_DESeq2(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots)
elif os.path.isfile(input_path):
DA_DESeq2(input_path, out_path, mapping_fp, mapping_category, subcategory_1, subcategory_2, DESeq2_diagnostic_plots)
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)
make_option('-i',
'--input_path',
type='existing_path',
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('-a',
'--algorithm',
default='metagenomeSeq_fitZIG',
type='choice',
choices=algorithm_list(),
help='differential abundance algorithm to '
'apply to input BIOM table(s) [default: %default]' +
' Available options are: '
'%s' % ', '.join(algorithm_list())),
make_option('-m',
'--mapping_file_path',
type='existing_filepath',
help='path to mapping file [REQUIRED if not passing -l]'),
make_option('-c',
'--mapping_file_category',
help='mapping file category [REQUIRED if not passing -l]'),
make_option('-x',
'--mapping_file_subcategory_1',
help='mapping file subcategory [REQUIRED if not passing -l]'),
make_option('-y',
"""Treatment:Fast groups.""",
"%prog -i otu_tables/ -o diff_otus/ -m map.txt -a metagenomeSeq_fitZIG -c Treatment -x Control -y Fast")
)
script_info['output_description']= "The resulting output OTU txt file contains a list of all the OTUs in the input matrix, along with their associated statistics and FDR p-values."
script_info['required_options']=[
]
script_info['optional_options']=[
make_option('-i', '--input_path', type='existing_path',
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('-a', '--algorithm', default='metagenomeSeq_fitZIG', type='choice',
choices=algorithm_list(), help='differential abundance algorithm to '
'apply to input BIOM table(s) [default: %default]' + ' Available options are: '
'%s' % ', '.join(algorithm_list())),
make_option('-m', '--mapping_file_path', type='existing_filepath',
help='path to mapping file [REQUIRED if not passing -l]'),
make_option('-c', '--mapping_file_category',
help='mapping file category [REQUIRED if not passing -l]'),
make_option('-x', '--mapping_file_subcategory_1',
help='mapping file subcategory [REQUIRED if not passing -l]'),
make_option('-y', '--mapping_file_subcategory_2',
help='mapping file subcategory [REQUIRED if not passing -l]'),
make_option('-l', '--list_algorithms', action='store_true', default=False,
help='show available differential abundance algorithms and exit '
'[default: %default]'),
make_option('-d', '--DESeq2_diagnostic_plots', default=False,
action='store_true', help='show a MA plot - y axis: log2 fold change, '
"""Treatment:Fast groups.""",
"%prog -i otu_tables/ -o diff_otus/ -m map.txt -a metagenomeSeq_fitZIG -c Treatment -x Control -y Fast")
)
script_info['output_description']= "The resulting output OTU txt file contains a list of all the OTUs in the input matrix, along with their associated statistics and FDR p-values."
script_info['required_options']=[
]
script_info['optional_options']=[
make_option('-i', '--input_path', type='existing_path',
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('-a', '--algorithm', default='metagenomeSeq_fitZIG', type='choice',
choices=algorithm_list(), help='differential abundance algorithm to '
'apply to input BIOM table(s) [default: %default]' + ' Available options are: '
'%s' % ', '.join(algorithm_list())),
make_option('-m', '--mapping_file_path', type='existing_filepath',
help='path to mapping file [REQUIRED if not passing -l]'),
make_option('-c', '--mapping_file_category',
help='mapping file category [REQUIRED if not passing -l]'),
make_option('-x', '--mapping_file_subcategory_1',
help='mapping file subcategory [REQUIRED if not passing -l]'),
make_option('-y', '--mapping_file_subcategory_2',
help='mapping file subcategory [REQUIRED if not passing -l]'),
make_option('-l', '--list_algorithms', action='store_true', default=False,
help='show available differential abundance algorithms and exit '
'[default: %default]'),
make_option('-d', '--DESeq2_diagnostic_plots', default=False,
action='store_true', help='show a MA plot - y axis: log2 fold change, '