def test_group_distances(self):
"""group_distances should return correct result.
"""
single_field_exp = {
'Treatment':
[[
'Control', 'Fast',
array([[0.729, 0.8, 0.721, 0.765],
[0.776, 0.744, 0.749, 0.677],
[0.734, 0.777, 0.733, 0.724],
[0.696, 0.675, 0.654, 0.696],
[0.731, 0.758, 0.738, 0.737]])
],
[
'Control', 'Control',
array([
0.625, 0.623, 0.61, 0.577, 0.615, 0.642, 0.673, 0.682,
0.737, 0.704
])
],
['Fast', 'Fast',
array([0.718, 0.666, 0.727, 0.6, 0.578, 0.623])]]
}
paired_field_exp = {
'Treatment_to_Treatment':
[[('Control', 'Control'), ('Fast', 'Fast'),
array([[0.729, 0.8, 0.721, 0.765], [0.776, 0.744, 0.749, 0.677],
[0.734, 0.777, 0.733,
0.724], [0.696, 0.675, 0.654, 0.696],
[0.731, 0.758, 0.738, 0.737]])],
[('Control', 'Control'), ('Control', 'Control'),
array([
0.625, 0.623, 0.61, 0.577, 0.615, 0.642, 0.673, 0.682, 0.737,
0.704
])],
[('Fast', 'Fast'), ('Fast', 'Fast'),
array([0.718, 0.666, 0.727, 0.6, 0.578, 0.623])]]
}
single_field_obs, paired_field_obs, dmat_obs = \
group_distances(mapping_file=self.map_file,
dmatrix_file=self.dmat_file,
fields=['Treatment'],
dir_prefix=self.working_dir)
self.assertEqual(single_field_exp, single_field_obs)
self.assertEqual(paired_field_exp, paired_field_obs)
self.assertEqual(self.dmat, dmat_obs)
def test_group_distances(self):
"""group_distances should return correct result.
"""
single_field_exp = {'Treatment':[\
['Control','Fast',array([[0.729, 0.8 , 0.721, 0.765],
[0.776, 0.744, 0.749, 0.677],
[0.734, 0.777, 0.733, 0.724],
[0.696, 0.675, 0.654, 0.696],
[0.731, 0.758, 0.738, 0.737]])],\
['Control','Control', array([0.625, 0.623, 0.61 , 0.577, 0.615,
0.642, 0.673, 0.682, 0.737, 0.704])],\
['Fast','Fast', array([0.718, 0.666, 0.727, 0.6, 0.578, 0.623])]
]}
paired_field_exp = {'Treatment_to_Treatment':[\
[('Control','Control'),('Fast','Fast'),\
array([[0.729, 0.8 , 0.721, 0.765],
[0.776, 0.744, 0.749, 0.677],
[0.734, 0.777, 0.733, 0.724],
[0.696, 0.675, 0.654, 0.696],
[0.731, 0.758, 0.738, 0.737]])],\
[('Control','Control'),('Control','Control'),\
array([0.625, 0.623, 0.61 , 0.577, 0.615,
0.642, 0.673, 0.682, 0.737, 0.704])],\
[('Fast','Fast'),('Fast','Fast'),\
array([0.718, 0.666, 0.727, 0.6, 0.578, 0.623])]
]}
single_field_obs, paired_field_obs, dmat_obs = \
group_distances(mapping_file=self.map_file,\
dmatrix_file=self.dmat_file,\
fields=['Treatment'],\
dir_prefix=self.working_dir)
self.assertEqual(single_field_exp,single_field_obs)
self.assertEqual(paired_field_exp,paired_field_obs)
self.assertEqual(self.dmat,dmat_obs)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Some code for error checking of input args:
# Check if distance_matrix_file is valid:
try:
d_header, d_mat = parse_distmat(open(opts.distance_matrix_file, "U"))
except:
option_parser.error(
"This does not look like a valid distance matrix file. Please supply a valid distance matrix file using the -d option."
)
if not is_symmetric_and_hollow(d_mat):
option_parser.error("The distance matrix must be symmetric and " "hollow.")
# Check if map_fname is valid:
try:
mapping, m_header, m_comments = parse_mapping_file(open(opts.map_fname, "U"))
except QiimeParseError:
option_parser.error(
"This does not look like a valid metadata mapping file. Please supply a valid mapping file using the -m option."
)
# make sure background_color is valid
if opts.background_color not in ["black", "white"]:
option_parser.error(
"'%s' is not a valid background color. Please pass in either 'black' or 'white' using the -k option."
% (opts.background_color)
)
# make sure prefs file is valid if it exists
if opts.prefs_path is not None:
try:
prefs_file = open(opts.prefs_path, "U").read()
except IOError:
option_parser.error(
"Provided prefs file, '%s', does not exist. Please pass in a valid prefs file with the -p option."
% (opts.prefs_path)
)
if opts.prefs_path is not None:
prefs = parse_prefs_file(prefs_file)
else:
prefs = None
color_prefs, color_data, background_color, label_color, ball_scale, arrow_colors = sample_color_prefs_and_map_data_from_options(
opts
)
# list of labelname, groups, colors, data_colors, data_color_order
groups_and_colors = list(iter_color_groups(mapping=color_data["map"], prefs=color_prefs))
# dict mapping labelname to list of: [groups, colors, data_colors,
# data_color_order]
field_to_colors = {}
for color_info in groups_and_colors:
field_to_colors[color_info[0]] = color_info[1:]
qiime_dir = get_qiime_project_dir() + "/qiime/support_files/"
fields = opts.fields
if fields is not None:
fields = map(strip, fields.split(","))
fields = [i.strip('"').strip("'") for i in fields]
elif prefs is not None:
fields = prefs.get("FIELDS", None)
else:
fields = get_interesting_mapping_fields(mapping, m_header)
# Check that all provided fields are valid:
if fields is not None:
for f in fields:
if f not in m_header:
option_parser.error(
"The field, %s, is not in the provided mapping file. Please supply correct fields (using the -f option or providing a 'FIELDS' list in the prefs file) corresponding to fields in mapping file."
% (f)
)
within_distances, between_distances, dmat = group_distances(
mapping_file=opts.map_fname,
dmatrix_file=opts.distance_matrix_file,
fields=fields,
dir_prefix=get_random_directory_name(output_dir=opts.dir_path, prefix="distances"),
)
if not opts.suppress_html_output:
# histograms output path
histograms_path = path.join(opts.dir_path, "histograms")
try:
mkdir(histograms_path)
except OSError: # raised if dir exists
pass
# draw all histograms
distances_dict, label_to_histogram_filename = draw_all_histograms(
single_field=within_distances,
paired_field=between_distances,
dmat=dmat,
histogram_dir=histograms_path,
field_to_color_prefs=field_to_colors,
background_color=background_color,
)
# Get relative path to histogram files.
label_to_histogram_filename_relative = _make_relative_paths(label_to_histogram_filename, opts.dir_path)
dm_fname = path.split(opts.distance_matrix_file)[-1]
basename = path.splitext(dm_fname)[0]
outfile_name = basename + "_distance_histograms.html"
make_main_html(
distances_dict=distances_dict,
label_to_histogram_filename=label_to_histogram_filename_relative,
root_outdir=opts.dir_path,
outfile_name=outfile_name,
title="Distance Histograms",
)
# Handle saving web resources locally.
# javascript file
javascript_path = path.join(opts.dir_path, "js")
try:
mkdir(javascript_path)
except OSError: # raised if dir exists
pass
js_out = open(javascript_path + "/histograms.js", "w")
js_out.write(open(qiime_dir + "js/histograms.js").read())
js_out.close()
monte_carlo_iters = opts.monte_carlo_iters
if monte_carlo_iters > 0:
# Do Monte Carlo for all fields
monte_carlo_group_distances(
mapping_file=opts.map_fname,
dmatrix_file=opts.distance_matrix_file,
prefs=prefs,
dir_prefix=opts.dir_path,
fields=fields,
default_iters=monte_carlo_iters,
)
# Do Monte Carlo for within and between fields
monte_carlo_group_distances_within_between(
single_field=within_distances,
paired_field=between_distances,
dmat=dmat,
dir_prefix=opts.dir_path,
num_iters=monte_carlo_iters,
)
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
#Some code for error checking of input args:
#Check if distance_matrix_file is valid:
try:
d_header, d_mat = parse_distmat(open(opts.distance_matrix_file, 'U'))
except:
option_parser.error(
"This does not look like a valid distance matrix file. Please supply a valid distance matrix file using the -d option."
)
if not is_symmetric_and_hollow(d_mat):
option_parser.error("The distance matrix must be symmetric and "
"hollow.")
#Check if map_fname is valid:
try:
mapping, m_header, m_comments = \
parse_mapping_file(open(opts.map_fname,'U'))
except QiimeParseError:
option_parser.error(
"This does not look like a valid metadata mapping file. Please supply a valid mapping file using the -m option."
)
#make sure background_color is valid
if opts.background_color not in ['black', 'white']:
option_parser.error(
"'%s' is not a valid background color. Please pass in either 'black' or 'white' using the -k option."
% (opts.background_color))
#make sure prefs file is valid if it exists
if opts.prefs_path is not None:
try:
prefs_file = open(opts.prefs_path, 'U').read()
except IOError:
option_parser.error(
"Provided prefs file, '%s', does not exist. Please pass in a valid prefs file with the -p option."
% (opts.prefs_path))
if opts.prefs_path is not None:
prefs = parse_prefs_file(prefs_file)
else:
prefs = None
color_prefs, color_data, background_color, label_color, ball_scale,\
arrow_colors=sample_color_prefs_and_map_data_from_options(opts)
#list of labelname, groups, colors, data_colors, data_color_order
groups_and_colors=list(iter_color_groups(mapping=color_data['map'],\
prefs=color_prefs))
#dict mapping labelname to list of: [groups, colors, data_colors,
# data_color_order]
field_to_colors = {}
for color_info in groups_and_colors:
field_to_colors[color_info[0]] = color_info[1:]
qiime_dir = get_qiime_project_dir() + '/qiime/support_files/'
fields = opts.fields
if fields is not None:
fields = map(strip, fields.split(','))
fields = [i.strip('"').strip("'") for i in fields]
elif prefs is not None:
fields = prefs.get('FIELDS', None)
else:
fields = get_interesting_mapping_fields(mapping, m_header)
#Check that all provided fields are valid:
if fields is not None:
for f in fields:
if f not in m_header:
option_parser.error(
"The field, %s, is not in the provided mapping file. Please supply correct fields (using the -f option or providing a 'FIELDS' list in the prefs file) corresponding to fields in mapping file."
% (f))
within_distances, between_distances, dmat = \
group_distances(mapping_file=opts.map_fname,\
dmatrix_file=opts.distance_matrix_file,\
fields=fields,\
dir_prefix=get_random_directory_name(output_dir=opts.dir_path,\
prefix='distances'))
if not opts.suppress_html_output:
#histograms output path
histograms_path = path.join(opts.dir_path, 'histograms')
try:
mkdir(histograms_path)
except OSError: #raised if dir exists
pass
#draw all histograms
distances_dict, label_to_histogram_filename = \
draw_all_histograms(single_field=within_distances, \
paired_field=between_distances, \
dmat=dmat,\
histogram_dir=histograms_path,\
field_to_color_prefs=field_to_colors,\
background_color=background_color)
#Get relative path to histogram files.
label_to_histogram_filename_relative = \
_make_relative_paths(label_to_histogram_filename, opts.dir_path)
dm_fname = path.split(opts.distance_matrix_file)[-1]
basename = path.splitext(dm_fname)[0]
outfile_name = basename + '_distance_histograms.html'
make_main_html(distances_dict=distances_dict,\
label_to_histogram_filename=label_to_histogram_filename_relative,\
root_outdir=opts.dir_path, \
outfile_name = outfile_name, \
title='Distance Histograms')
#Handle saving web resources locally.
#javascript file
javascript_path = path.join(opts.dir_path, 'js')
try:
mkdir(javascript_path)
except OSError: #raised if dir exists
pass
js_out = open(javascript_path + '/histograms.js', 'w')
js_out.write(open(qiime_dir + 'js/histograms.js').read())
js_out.close()
monte_carlo_iters = opts.monte_carlo_iters
if monte_carlo_iters > 0:
#Do Monte Carlo for all fields
monte_carlo_group_distances(mapping_file=opts.map_fname,\
dmatrix_file=opts.distance_matrix_file,\
prefs=prefs, \
dir_prefix = opts.dir_path,\
fields=fields,\
default_iters=monte_carlo_iters)
#Do Monte Carlo for within and between fields
monte_carlo_group_distances_within_between(\
single_field=within_distances,\
paired_field=between_distances, dmat=dmat, \
dir_prefix = opts.dir_path,\
num_iters=monte_carlo_iters)
