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()),))
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()),))
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)