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()),))
print("For more information, see http://scikit-bio.org/docs/latest/ge"
"nerated/skbio.diversity.alpha.html#module-skbio.diversity.alpha")
exit(0)
almost_required_options = ['input_path', 'output_path', 'metrics']
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if os.path.isdir(opts.input_path):
multiple_file_alpha(opts.input_path, opts.output_path, opts.metrics,
opts.tree_path)
elif os.path.isfile(opts.input_path):
try:
f = open(opts.output_path, 'w')
f.close()
except IOError:
if os.path.isdir(opts.output_path):
option_parser.error(
"ioerror, couldn't create output file. The output path is a directory, which should be a single file")
else:
option_parser.error("ioerror, couldn't create output file")
single_file_alpha(opts.input_path, opts.metrics,
opts.output_path, opts.tree_path)
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()),))
print(
"For more information, see http://qiime.org/scripts/alpha_diversity_metrics.html"
)
exit(0)
almost_required_options = ['input_path', 'output_path', 'metrics']
for option in almost_required_options:
if getattr(opts, option) == None:
option_parser.error('Required option --%s omitted.' % option)
if os.path.isdir(opts.input_path):
multiple_file_alpha(opts.input_path, opts.output_path, opts.metrics,
opts.tree_path)
elif os.path.isfile(opts.input_path):
try:
f = open(opts.output_path, 'w')
f.close()
except IOError:
if os.path.isdir(opts.output_path):
option_parser.error(
"ioerror, couldn't create output file. The output path is a directory, which should be a single file"
)
else:
option_parser.error("ioerror, couldn't create output file")
single_file_alpha(opts.input_path, opts.metrics, opts.output_path,
opts.tree_path)
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()),))
print("For more information, see http://qiime.org/scripts/alpha_diversity_metrics.html")
exit(0)
almost_required_options = ['input_path','output_path','metrics']
for option in almost_required_options:
if getattr(opts,option) == None:
option_parser.error('Required option --%s omitted.' % option)
if os.path.isdir(opts.input_path):
multiple_file_alpha(opts.input_path, opts.output_path, opts.metrics,
opts.tree_path)
elif os.path.isfile(opts.input_path):
try:
f = open(opts.output_path, 'w')
f.close()
except IOError:
print("ioerror, couldn't create output file")
exit(1)
single_file_alpha(opts.input_path, opts.metrics,
opts.output_path, opts.tree_path)
else:
print("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_path', 'metrics']
for option in almost_required_options:
if getattr(opts, option) == None:
option_parser.error('Required option --%s omitted.' % option)
if os.path.isdir(opts.input_path):
multiple_file_alpha(opts.input_path, opts.output_path, opts.metrics,
opts.tree_path)
elif os.path.isfile(opts.input_path):
try:
f = open(opts.output_path, 'w')
f.close()
except IOError:
print("ioerror, couldn't create output file")
exit(1)
single_file_alpha(opts.input_path, opts.metrics, opts.output_path,
opts.tree_path)
else:
print("io error, input path not valid. does it exist?")
exit(1)
PC.635 0.94 4.20239 18.0
PC.636 0.925 3.78882 16.0
====== ======= ============= ================
"""
script_info['required_options'] = []
script_info['optional_options']=[\
make_option('-i', '--input_path',
help='Input OTU table filepath or input directory containing OTU' +\
' tables for batch processing. [default: %default]',
type='existing_path'),
make_option('-o', '--output_path',
help='Output filepath to store alpha diversity metric(s) for each sample in a tab-separated format' +\
'or output directory when batch processing. [default: %default]',
type='new_path'),
make_option('-m', '--metrics', type='multiple_choice',
mchoices=list_known_metrics(),
default='PD_whole_tree,chao1,observed_species',
help='Alpha-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',
dest="show_metrics",
help='Show the available alpha-diversity metrics and exit.'),
make_option('-t', '--tree_path', default=None,
help='Input newick tree filepath.' +\
' [default: %default; REQUIRED for phylogenetic metrics]',
type='existing_filepath')
]
script_info['version'] = __version__
PC.635 0.94 4.20239 18.0
PC.636 0.925 3.78882 16.0
====== ======= ============= =============
"""
script_info['required_options'] = []
script_info['optional_options'] = [
make_option('-i', '--input_path',
help='Input OTU table filepath or input directory containing OTU' +
' tables for batch processing. [default: %default]',
type='existing_path'),
make_option('-o', '--output_path',
help='Output filepath to store alpha diversity metric(s) for each sample in a tab-separated format '
'or output directory when batch processing. [default: %default]',
type='new_path'),
make_option('-m', '--metrics', type='multiple_choice',
mchoices=list_known_metrics(),
default='PD_whole_tree,chao1,observed_otus',
help='Alpha-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',
dest="show_metrics",
help='Show the available alpha-diversity metrics and exit.'),
make_option('-t', '--tree_path', default=None,
help='Input newick tree filepath.' +
' [default: %default; REQUIRED for phylogenetic metrics]',
type='existing_filepath')
]
script_info['version'] = __version__
__maintainer__ = "Jesse Stombaugh"
__email__ = "*****@*****.**"
__status__ = "Development"
from cogent.util.unit_test import TestCase, main
import os, sys, copy
from qiime.util import get_qiime_scripts_dir,make_option
from html_from_script import script_path_components,get_script_info,\
_format_help,generate_choice_input,\
generate_string_input,generate_float_input,\
generate_int_input,generate_True_input,\
generate_False_input,get_html_for_options,get_html
from qiime.alpha_diversity import list_known_metrics
alpha_metrics=list_known_metrics();
from qiime.beta_diversity import list_known_metrics
beta_metrics=list_known_metrics();
class HTMLFromScriptTests(TestCase):
def setUp(self):
""" """
self.headers=['head1','head2','head3']
self.test_option_file=make_option('-i', '--coord_fname',
help='Input principal coordinates filepath',
type='existing_path')
self.test_option_colorby=make_option('-b', '--colorby', dest='colorby',\
help='Comma-separated list categories metadata categories' +\