def main():
# parse command line
option_parser, opts, args = parse_command_line_parameters(**script_info)
# ensure metadata is present and real-valued
validate_metadata(opts.map_fp, opts.gradient_variable)
# run detrending
detrend_pcoa(opts.input_fp,
map_fp=opts.map_fp,
gradient_variable=opts.gradient_variable,
suppress_prerotate=opts.suppress_prerotate,
output_dir=opts.output_dir)
def test_detrend_gradient_no_prerotate(self):
"""Ensure that detrending runs and produces expected files
with associated gradient.
"""
results = detrend_pcoa(
input_fp=self.tmp_pc_fp,
map_fp=self.tmp_map_fp,
gradient_variable="Gradient",
suppress_prerotate=True,
output_dir=self.output_dir,
HALT_EXEC=False,
)
# check formatting of summary file
lines = results["summary"].readlines()
self.assertEqual(len(lines), 4)
# check formatting of coords file
lines = results["coords"].readlines()
# ensure one line per sample in detrended pcoa
self.assertEqual(len(lines), len(test_pc.split("\n")) - 4)
# ensure three columns tab delimited
self.assertEqual(len(lines[0].split("\t")), 3)
# ensure that plot pdf is at least present
self.assertEqual(str(type(results["plot"])), "<type 'file'>")
def test_detrend_gradient(self):
"""Ensure that detrending runs and produces expected files
with associated gradient.
"""
results = detrend_pcoa(input_fp=self.tmp_pc_fp,
map_fp=self.tmp_map_fp,
gradient_variable='Gradient',
suppress_prerotate=False,
output_dir=self.output_dir,
HALT_EXEC=False)
# check formatting of summary file
lines = results['summary'].readlines()
self.assertEqual(len(lines), 4)
# check formatting of coords file
lines = results['coords'].readlines()
# ensure one line per sample in detrended pcoa
self.assertEqual(len(lines), len(test_pc.split('\n')) - 4)
# ensure three columns tab delimited
self.assertEqual(len(lines[0].split('\t')), 3)
# ensure that plot pdf is at least present
self.assertEqual(str(type(results['plot'])), "<type 'file'>")
def main():
# parse command line
option_parser, opts, args = parse_command_line_parameters(**script_info)
# can't pass map without column header
if opts.map_fp is not None and opts.gradient_variable is None:
option_parser.error("Cannot pass -m/--map_fp without -c/--gradient_variable.")
# ensure metadata is present and real-valued
if opts.map_fp is not None:
validate_metadata(opts.map_fp, opts.gradient_variable)
# run detrending
detrend_pcoa(opts.input_fp,
map_fp=opts.map_fp,
gradient_variable=opts.gradient_variable,
suppress_prerotate=opts.suppress_prerotate,
output_dir=opts.output_dir)
def main():
# parse command line
option_parser, opts, args = parse_command_line_parameters(**script_info)
# can't pass map without column header
if opts.map_fp is not None and opts.gradient_variable is None:
option_parser.error("Cannot pass -m/--map_fp without -c/--gradient_variable.")
# ensure metadata is present and real-valued
if opts.map_fp is not None:
validate_metadata(opts.map_fp, opts.gradient_variable)
# run detrending
detrend_pcoa(opts.input_fp,
map_fp=opts.map_fp,
gradient_variable=opts.gradient_variable,
suppress_prerotate=opts.suppress_prerotate,
output_dir=opts.output_dir)
def test_detrend_no_gradient(self):
"""Ensure that detrending runs and produces expected files
with no associated gradient.
"""
results = detrend_pcoa(input_fp=self.tmp_pc_fp,
map_fp=None, gradient_variable=None,
suppress_prerotate=False, output_dir=self.output_dir,
HALT_EXEC=False)
self.assertEqual(results['summary'], None)
coords = results['coords']
lines = coords.readlines()
# ensure one line per sample in detrended pcoa
self.assertEqual(len(lines), len(test_pc.split('\n')) - 4)
# ensure three columns tab delimited
self.assertEqual(len(lines[0].split('\t')), 3)
def test_detrend_no_gradient(self):
"""Ensure that detrending runs and produces expected files
with no associated gradient.
"""
results = detrend_pcoa(input_fp=self.tmp_pc_fp,
map_fp=None, gradient_variable=None,
suppress_prerotate=False, output_dir=self.output_dir,
HALT_EXEC=False)
self.assertEqual(results['summary'], None)
coords = results['coords']
lines = coords.readlines()
# ensure one line per sample in detrended pcoa
self.assertEqual(len(lines), len(test_pc.split('\n')) - 4)
# ensure three columns tab delimited
self.assertEqual(len(lines[0].split('\t')), 3)