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_cup_metrics()), ))
exit(0)
almost_required_options = ['input_path', 'output_path']
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error('Required option --%s omitted.' % option)
if os.path.isfile(opts.input_path):
try:
f = open(opts.output_path, 'w')
except IOError:
exit("ioerror, couldn't create output file")
f.close()
single_file_cup(opts.input_path, opts.metrics, opts.output_path,
opts.look_ahead)
else:
exit("io error, input path not valid. does it exist?")
def test_single_file_cup_string(self):
"""Returns matrix with estimates using metrics string."""
# convert_biom using otu_table w/o leading #
bt_string = (
'{"rows": [{"id": "1", "metadata": null}, {"id": "2",'
'"metadata": null}, {"id": "3", "metadata": null}, {"id": "4", '
'"metadata": null}, {"id": "5", "metadata": null}], "format": '
'"Biological Observation Matrix 0.9.1-dev", "data": [[0, 0, 3.0], '
'[0, 1, 4.0], [1, 0, 2.0], [1, 1, 5.0], [2, 0, 1.0], [2, 1, 2.0], '
'[3, 1, 4.0], [4, 0, 1.0]], "columns": [{"id": "S1", "metadata": '
'null}, {"id": "S2", "metadata": null}], "generated_by": '
'"BIOM-Format 0.9.1-dev", "matrix_type": "sparse", "shape": '
'[5, 2], "format_url": "http://biom-format.org", "date": '
'"2012-05-04T09:28:28.247809", "type": "OTU table", "id": null, '
'"matrix_element_type": "float"}')
with open(self.tmp_file, 'w') as fh:
fh.write(bt_string)
single_file_cup(self.tmp_file, 'lladser_pe,lladser_ci',
self.tmp_outfile, r=4)
# Not much testing here, just make sure we get back a (formatted)
# matrix with the right dimensions
with open(self.tmp_outfile, 'U') as out_f:
observed = out_f.readlines()
self.assertEqual(len(observed), 3)
self.assertEqual(len(observed[1].split('\t')), 4)
def test_single_file_cup_string(self):
"""Returns matrix with estimates using metrics string."""
# convert_biom using otu_table w/o leading #
bt_string = (
'{"rows": [{"id": "1", "metadata": null}, {"id": "2",'
'"metadata": null}, {"id": "3", "metadata": null}, {"id": "4", '
'"metadata": null}, {"id": "5", "metadata": null}], "format": '
'"Biological Observation Matrix 0.9.1-dev", "data": [[0, 0, 3.0], '
'[0, 1, 4.0], [1, 0, 2.0], [1, 1, 5.0], [2, 0, 1.0], [2, 1, 2.0], '
'[3, 1, 4.0], [4, 0, 1.0]], "columns": [{"id": "S1", "metadata": '
'null}, {"id": "S2", "metadata": null}], "generated_by": '
'"BIOM-Format 0.9.1-dev", "matrix_type": "sparse", "shape": '
'[5, 2], "format_url": "http://biom-format.org", "date": '
'"2012-05-04T09:28:28.247809", "type": "OTU table", "id": null, '
'"matrix_element_type": "float"}')
with open(self.tmp_file, 'w') as fh:
fh.write(bt_string)
single_file_cup(self.tmp_file,
'lladser_pe,lladser_ci',
self.tmp_outfile,
r=4)
# Not much testing here, just make sure we get back a (formatted)
# matrix with the right dimensions
with open(self.tmp_outfile, 'U') as out_f:
observed = out_f.readlines()
self.assertEqual(len(observed), 3)
self.assertEqual(len(observed[1].split('\t')), 4)
def test_single_file_cup_list(self):
"""Returns matrix with estimates using metrics list."""
# convert_biom using otu_table w/o leading #
bt_string = (
'{"rows": [{"id": "1", "metadata": null}], "format": "Biological '
'Observation Matrix 0.9.1-dev", "data": [[0, 0, 3.0]], "columns": '
'[{"id": "S1", "metadata": null}], "generated_by": '
'"BIOM-Format 0.9.1-dev", "matrix_type": "sparse", "shape": '
'[1, 1], "format_url": "http://biom-format.org", "date": '
'"2012-05-04T09:36:57.500673", "type": "OTU table", "id": null, '
'"matrix_element_type": "float"}')
with open(self.tmp_file, 'w') as fh:
fh.write(bt_string)
single_file_cup(self.tmp_file, ['lladser_pe', 'lladser_ci'],
self.tmp_outfile,
r=4)
with open(self.tmp_outfile, 'U') as out_f:
observed = out_f.readlines()
expected = [
"\tlladser_pe\tlladser_lower_bound\tlladser_upper_bound\n",
"S1\tnan\tnan\tnan\n"
]
self.assertEqual(observed, expected)
def test_single_file_cup_list(self):
"""Returns matrix with estimates using metrics list."""
# convert_biom using otu_table w/o leading #
bt_string = (
'{"rows": [{"id": "1", "metadata": null}], "format": "Biological '
'Observation Matrix 0.9.1-dev", "data": [[0, 0, 3.0]], "columns": '
'[{"id": "S1", "metadata": null}], "generated_by": '
'"BIOM-Format 0.9.1-dev", "matrix_type": "sparse", "shape": '
'[1, 1], "format_url": "http://biom-format.org", "date": '
'"2012-05-04T09:36:57.500673", "type": "OTU table", "id": null, '
'"matrix_element_type": "float"}')
with open(self.tmp_file, 'w') as fh:
fh.write(bt_string)
single_file_cup(self.tmp_file, ['lladser_pe', 'lladser_ci'],
self.tmp_outfile, r=4, alpha=0.95, f=10,
ci_type="ULCL")
with open(self.tmp_outfile, 'U') as out_f:
observed = out_f.readlines()
expected = ["\tlladser_pe\tlladser_lower_bound\tlladser_upper_bound\n",
"S1\tNaN\tNaN\tNaN"]
self.assertEqual(observed, expected)
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_cup_metrics()),))
exit(0)
almost_required_options = ['input_path', 'output_path']
for option in almost_required_options:
if getattr(opts,option) == None:
option_parser.error('Required option --%s omitted.' % option)
if os.path.isfile(opts.input_path):
try:
f = open(opts.output_path, 'w')
except IOError:
exit("ioerror, couldn't create output file")
f.close()
single_file_cup(opts.input_path, opts.metrics, opts.output_path,
opts.look_ahead, opts.alpha, opts.f_ratio, opts.ci_type)
else:
exit("io error, input path not valid. does it exist?")
def test_single_file_cup(self):
"""single_file_cup returns matrix with estimates"""
# Test using a string as metrics
# convert_biom using otu_table w/o leading #
bt_string = '{"rows": [{"id": "1", "metadata": null}, {"id": "2",\
"metadata": null}, {"id": "3", "metadata": null}, {"id": "4", "metadata":\
null}, {"id": "5", "metadata": null}], "format": "Biological Observation\
Matrix 0.9.1-dev", "data": [[0, 0, 3.0], [0, 1, 4.0], [1, 0, 2.0],\
[1, 1, 5.0], [2, 0, 1.0], [2, 1, 2.0], [3, 1, 4.0], [4, 0, 1.0]], "columns":\
[{"id": "S1", "metadata": null}, {"id": "S2", "metadata": null}],\
"generated_by": "BIOM-Format 0.9.1-dev", "matrix_type": "sparse", "shape":\
[5, 2], "format_url": "http://biom-format.org", "date":\
"2012-05-04T09:28:28.247809", "type": "OTU table", "id": null,\
"matrix_element_type": "float"}'
fh = open(self.tmp_file, "w")
fh.write(bt_string)
fh.close()
self.files_to_remove.append(self.tmp_file)
self.files_to_remove.append(self.tmp_outfile)
# Not much testing here, just make sure we get back a (formatted)
# matrix with the right dimensions
single_file_cup(self.tmp_file,
'lladser_pe,lladser_ci',
self.tmp_outfile,
r=4,
alpha=0.95,
f=10,
ci_type="ULCL")
observed = open(self.tmp_outfile, "U").readlines()
self.assertEqual(len(observed), 3)
self.assertEqual(len(observed[1].split('\t')), 4)
# Test using a list as metrics
# convert_biom using otu_table w/o leading #
bt_string = '{"rows": [{"id": "1", "metadata": null}], "format":\
"Biological Observation Matrix 0.9.1-dev", "data": [[0, 0, 3.0]], "columns":\
[{"id": "S1", "metadata": null}], "generated_by": "BIOM-Format 0.9.1-dev",\
"matrix_type": "sparse", "shape": [1, 1], "format_url":\
"http://biom-format.org", "date": "2012-05-04T09:36:57.500673", "type":\
"OTU table", "id": null, "matrix_element_type": "float"}'
fh = open(self.tmp_file, "w")
fh.write(bt_string)
fh.close()
single_file_cup(self.tmp_file, ['lladser_pe', 'lladser_ci'],
self.tmp_outfile,
r=4,
alpha=0.95,
f=10,
ci_type="ULCL")
observed = open(self.tmp_outfile, "U").readlines()
expected = [
"\tlladser_pe\tlladser_lower_bound\tlladser_upper_bound\n",
"S1\tNaN\tNaN\tNaN"
]
self.assertEqual(observed, expected)
def test_single_file_cup(self):
"""single_file_cup returns matrix with estimates"""
# Test using a string as metrics
# convert_biom using otu_table w/o leading #
bt_string = '{"rows": [{"id": "1", "metadata": null}, {"id": "2",\
"metadata": null}, {"id": "3", "metadata": null}, {"id": "4", "metadata":\
null}, {"id": "5", "metadata": null}], "format": "Biological Observation\
Matrix 0.9.1-dev", "data": [[0, 0, 3.0], [0, 1, 4.0], [1, 0, 2.0],\
[1, 1, 5.0], [2, 0, 1.0], [2, 1, 2.0], [3, 1, 4.0], [4, 0, 1.0]], "columns":\
[{"id": "S1", "metadata": null}, {"id": "S2", "metadata": null}],\
"generated_by": "BIOM-Format 0.9.1-dev", "matrix_type": "sparse", "shape":\
[5, 2], "format_url": "http://biom-format.org", "date":\
"2012-05-04T09:28:28.247809", "type": "OTU table", "id": null,\
"matrix_element_type": "float"}'
fh = open(self.tmp_file,"w")
fh.write(bt_string)
fh.close()
self.files_to_remove.append(self.tmp_file)
self.files_to_remove.append(self.tmp_outfile)
# Not much testing here, just make sure we get back a (formatted)
# matrix with the right dimensions
single_file_cup(self.tmp_file, 'lladser_pe,lladser_ci',
self.tmp_outfile, r=4, alpha=0.95, f=10, ci_type="ULCL")
observed = open(self.tmp_outfile,"U").readlines()
self.assertEqual(len(observed), 3)
self.assertEqual(len(observed[1].split('\t')), 4)
# Test using a list as metrics
# convert_biom using otu_table w/o leading #
bt_string = '{"rows": [{"id": "1", "metadata": null}], "format":\
"Biological Observation Matrix 0.9.1-dev", "data": [[0, 0, 3.0]], "columns":\
[{"id": "S1", "metadata": null}], "generated_by": "BIOM-Format 0.9.1-dev",\
"matrix_type": "sparse", "shape": [1, 1], "format_url":\
"http://biom-format.org", "date": "2012-05-04T09:36:57.500673", "type":\
"OTU table", "id": null, "matrix_element_type": "float"}'
fh = open(self.tmp_file,"w")
fh.write(bt_string)
fh.close()
single_file_cup(self.tmp_file, ['lladser_pe','lladser_ci'],
self.tmp_outfile, r=4, alpha=0.95, f=10, ci_type="ULCL")
observed = open(self.tmp_outfile,"U").readlines()
expected=["\tlladser_pe\tlladser_lower_bound\tlladser_upper_bound\n",
"S1\tNaN\tNaN\tNaN"]
self.assertEqual(observed, expected)
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_cup_metrics()),))
exit(0)
almost_required_options = ["input_path", "output_path"]
for option in almost_required_options:
if getattr(opts, option) is None:
option_parser.error("Required option --%s omitted." % option)
if os.path.isfile(opts.input_path):
try:
f = open(opts.output_path, "w")
except IOError:
exit("ioerror, couldn't create output file")
f.close()
single_file_cup(opts.input_path, opts.metrics, opts.output_path, opts.look_ahead)
else:
exit("io error, input path not valid. does it exist?")
