def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.show_metrics:
print("Known metrics are: %s\n"
% (', '.join(list_known_metrics()),))
exit(0)
almost_required_options = ['input_path', 'output_dir', 'metrics']
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if opts.output_dir.endswith('.txt'):
stderr.write('output must be a directory, files will be named' +
' automatically. And we refuse to make .txt directories\n')
exit(1)
if opts.tree_path == "None":
opts.tree_path = None
try:
os.makedirs(opts.output_dir)
except OSError:
pass # hopefully dir already exists
if os.path.isdir(opts.input_path):
multiple_file_beta(opts.input_path, opts.output_dir, opts.metrics,
opts.tree_path, opts.rows, full_tree=opts.full_tree)
elif os.path.isfile(opts.input_path):
single_file_beta(opts.input_path, opts.metrics, opts.tree_path,
opts.output_dir, opts.rows, full_tree=opts.full_tree)
else:
stderr.write("io error, input path not valid. Does it exist?")
exit(1)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
if opts.show_metrics:
print("Known metrics are: %s\n"
% (', '.join(list_known_metrics()),))
exit(0)
almost_required_options = ['input_path', 'output_dir', 'metrics']
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if opts.output_dir.endswith('.txt'):
stderr.write('output must be a directory, files will be named' +
' automatically. And we refuse to make .txt directories\n')
exit(1)
if opts.tree_path == "None":
opts.tree_path = None
try:
os.makedirs(opts.output_dir)
except OSError:
pass # hopefully dir already exists
if os.path.isdir(opts.input_path):
multiple_file_beta(opts.input_path, opts.output_dir, opts.metrics,
opts.tree_path, opts.rows, full_tree=opts.full_tree)
elif os.path.isfile(opts.input_path):
single_file_beta(opts.input_path, opts.metrics, opts.tree_path,
opts.output_dir, opts.rows, full_tree=opts.full_tree)
else:
stderr.write("io error, input path not valid. Does it exist?")
exit(1)
"output_description"
] = """The output of %prog is a folder containing\
text files, each a distance matrix between samples."""
script_info["required_options"] = [
make_option("-i", "--input_path", type="existing_path", help="input path, must be directory [REQUIRED]"),
make_option("-o", "--output_path", type="new_dirpath", help="output path, must be directory [REQUIRED]"),
]
script_info["optional_options"] = [
make_option(
"-m",
"--metrics",
default="unweighted_unifrac,weighted_unifrac",
type="multiple_choice",
mchoices=list_known_metrics(),
help="Beta-diversity metric(s) to use. A comma-separated list should be"
+ " provided when multiple metrics are specified. [default: %default]",
),
make_option(
"-t",
"--tree_path",
type="existing_filepath",
help="path to newick tree file, required for phylogenetic metrics" + " [default: %default]",
),
options_lookup["retain_temp_files"],
options_lookup["suppress_submit_jobs"],
options_lookup["poll_directly"],
options_lookup["cluster_jobs_fp"],
options_lookup["suppress_polling"],
options_lookup["job_prefix"],
table."""
script_info['required_options'] = []
script_info['optional_options']=[
make_option('-i', '--input_path',
help='Input OTU table in biom format or input directory containing OTU ' +\
'tables in biom format for batch processing.',
type='existing_path'),
make_option('-r', '--rows', default=None, type='string',
help='Compute for only these rows of the distance matrix.' +\
' User should pass a list of sample names (e.g. "s1,s3")' +\
' [default: %default; full n x n matrix is generated]'),
make_option('-o', '--output_dir',
help="Output directory. One will be created if it doesn't exist.",
type='new_dirpath'),
make_option('-m', '--metrics', default='unweighted_unifrac,weighted_unifrac',
type='multiple_choice', mchoices=list_known_metrics(),
help='Beta-diversity metric(s) to use. A comma-separated list should' +\
' be provided when multiple metrics are specified. [default: %default]'),
make_option('-s', '--show_metrics', action='store_true', default=False,
help='Show the available beta-diversity metrics and exit. Metrics' +\
' starting with' +\
' "binary..." specifies that a metric is qualitative, and considers' +\
' only the presence or absence of each taxon [default: %default]'),
make_option('-t', '--tree_path', default=None,
help='Input newick tree filepath, which is required when phylogenetic' +\
' metrics are specified. [default: %default]',
type='existing_filepath'),
make_option('-f', '--full_tree', action="store_true", default=False,
help='By default, tips not corresponding to OTUs in the OTU table are '+\
'removed from the tree for diversity calculations. ' +\
'Pass to skip this step if you\'re already passing a minimal tree.' +\
("""Apply beta_diversity.py in parallel to a single otu table""",""" """,
"""%prog -i $PWD/otu_table.biom -o $PWD/bdiv_single/ -t $PWD/rep_set.tre"""))
script_info['output_description']="""The output of %prog is a folder containing\
text files, each a distance matrix between samples."""
script_info['required_options'] = [\
make_option('-i', '--input_path',type='existing_path',
help='input path, must be directory [REQUIRED]'),\
make_option('-o', '--output_path',type='new_dirpath',
help='output path, must be directory [REQUIRED]'),
]
script_info['optional_options'] = [
make_option('-m', '--metrics', default='unweighted_unifrac,weighted_unifrac',
type='multiple_choice', mchoices=list_known_metrics(),
help='Beta-diversity metric(s) to use. A comma-separated list should be' +\
' provided when multiple metrics are specified. [default: %default]'),
make_option('-t', '--tree_path', type='existing_filepath',
help='path to newick tree file, required for phylogenetic metrics'+\
' [default: %default]'),\
options_lookup['retain_temp_files'],
options_lookup['suppress_submit_jobs'],
options_lookup['poll_directly'],
options_lookup['cluster_jobs_fp'],
options_lookup['suppress_polling'],
options_lookup['job_prefix'],
options_lookup['seconds_to_sleep'],
options_lookup['jobs_to_start'],
make_option('-f', '--full_tree', action="store_true",
help='By default, each job removes calls _fast_unifrac_setup to remove\
default=None,
type='string',
help='Compute for only these rows of the distance matrix.' +
' User should pass a list of sample names (e.g. "s1,s3")' +
' [default: %default; full n x n matrix is generated]'),
make_option(
'-o',
'--output_dir',
help="Output directory. One will be created if it doesn't exist.",
type='new_dirpath'),
make_option(
'-m',
'--metrics',
default='unweighted_unifrac,weighted_unifrac',
type='multiple_choice',
mchoices=list_known_metrics(),
help='Beta-diversity metric(s) to use. A comma-separated list should' +
' be provided when multiple metrics are specified. [default: %default]'
),
make_option(
'-s',
'--show_metrics',
action='store_true',
default=False,
help='Show the available beta-diversity metrics and exit. Metrics' +
' starting with' +
' "binary..." specifies that a metric is qualitative, and considers' +
' only the presence or absence of each taxon [default: %default]'),
make_option(
'-t',
'--tree_path',
