def test_make_averages(self):
'''make_averages: this tests the main function in make_rarefaction_plots
and returns an html output'''
filename1='/tmp/html_plots/testcol_0_row_0_ave.png'
folder1='/tmp/html_plots'
filename3='/tmp/average_tables/testSampleID.txt'
folder2='/tmp/average_tables'
filename4='/tmp/average_plots/testSampleID.png'
folder3='/tmp/average_plots'
self._paths_to_clean_up = [filename1,filename3,filename4]
self._folders_to_cleanup = [folder1,folder2,folder3]
obs=make_averages(self.color_prefs,self.data,self.background_color, \
self.label_color,self.rares,self.output_dir, \
self.resolution,self.imagetype,None,False, \
self.std_type)
self.assertEqual(obs,exp_html)
self.assertTrue(exists(filename1))
self.assertTrue(exists(filename3))
self.assertTrue(exists(filename4))
self.assertTrue(exists(folder1))
self.assertTrue(exists(folder2))
self.assertTrue(exists(folder3))
def test_make_averages(self):
'''make_averages: this tests the main function in make_rarefaction_plots
and returns an html output'''
filename1 = '/tmp/html_plots/testcol_0_row_0_ave.png'
folder1 = '/tmp/html_plots'
filename3 = '/tmp/average_tables/testSampleID.txt'
folder2 = '/tmp/average_tables'
filename4 = '/tmp/average_plots/testSampleID.png'
folder3 = '/tmp/average_plots'
self._paths_to_clean_up = [filename1, filename3, filename4]
self._folders_to_cleanup = [folder1, folder2, folder3]
obs=make_averages(self.color_prefs,self.data,self.background_color, \
self.label_color,self.rares,self.output_dir, \
self.resolution,self.imagetype,None,False, \
self.std_type)
self.assertEqual(obs, exp_html)
self.assertTrue(exists(filename1))
self.assertTrue(exists(filename3))
self.assertTrue(exists(filename4))
self.assertTrue(exists(folder1))
self.assertTrue(exists(folder2))
self.assertTrue(exists(folder3))
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
input_dir = opts.input_dir
imagetype = opts.imagetype
resolution = opts.resolution
output_dir = opts.output_dir
ymax = opts.ymax
std_type = opts.std_type
suppress_webpage = opts.suppress_html_output
output_type = opts.output_type
generate_per_sample_plots = opts.generate_per_sample_plots
generate_average_tables = opts.generate_average_tables
# Get the command-line options.
prefs, data, background_color, label_color, ball_scale, arrow_colors = \
sample_color_prefs_and_map_data_from_options(opts)
rares = {}
if isdir(input_dir):
rarenames = listdir(input_dir)
rarenames = [r for r in rarenames if not r.startswith('.')]
for r in rarenames:
try:
rarefl = open(path.join(input_dir, r), 'U').readlines()
rares[r] = parse_rarefaction(rarefl)
except(IOError):
option_parser.error('Problem with rarefaction file. %s' %
exc_info()[1])
exit(0)
else:
try:
input_file = input_dir.split(',')
for i in range(len(input_file)):
input_path = split(input_file[i])[-1]
rarefl = open(input_file[i], 'U').readlines()
rares[input_path] = parse_rarefaction(rarefl)
except(IOError):
option_parser.error('Problem with rarefaction file. %s' %
exc_info()[1])
exit(0)
if imagetype not in ['png', 'svg', 'pdf']:
option_parser.error('Supplied extension not supported.')
exit(0)
try:
resolution = int(resolution)
except(ValueError):
option_parser.error('Inavlid resolution.')
exit(0)
# output directory check
if isinstance(output_dir, str) and output_dir != '.':
if exists(output_dir):
output_dir = output_dir
else:
try:
create_dir(output_dir, False)
output_dir = output_dir
except(ValueError):
option_parser.error('Could not create output directory.')
exit(0)
else:
output_dir = get_random_directory_name()
# Generate the plots and html text
html_output = make_averages(prefs, data, background_color, label_color,
rares, output_dir, resolution, imagetype, ymax,
suppress_webpage, std_type, output_type,
generate_per_sample_plots=generate_per_sample_plots,
generate_average_tables=generate_average_tables)
if html_output:
# Write the html file.
outfile = open(path.join(output_dir, 'rarefaction_plots.html'), 'w')
outfile.write(html_output)
outfile.close()
def main():
option_parser, options, args = parse_command_line_parameters(**script_info)
ops = {}
input_dir = options.input_dir
rares = {}
if isdir(input_dir):
rarenames = listdir(input_dir)
rarenames = [r for r in rarenames if not r.startswith(".")]
for r in rarenames:
try:
rarefl = open(path.join(input_dir, r), "U").readlines()
rares[r] = parse_rarefaction(rarefl)
except (IOError):
option_parser.error("Problem with rarefaction file. %s" % exc_info()[1])
exit(0)
else:
try:
input_file = input_dir.split(",")
for i in range(len(input_file)):
input_path = split(input_file[i])[-1]
rarefl = open(input_file[i], "U").readlines()
rares[input_path] = parse_rarefaction(rarefl)
except (IOError):
option_parser.error("Problem with rarefaction file. %s" % exc_info()[1])
exit(0)
if options.imagetype not in ["png", "svg", "pdf"]:
option_parser.error("Supplied extension not supported.")
exit(0)
else:
imagetype = options.imagetype
try:
resolution = int(options.resolution)
except (ValueError):
option_parser.error("Inavlid resolution.")
exit(0)
# Get the command-line options.
prefs, data, background_color, label_color, ball_scale, arrow_colors = sample_color_prefs_and_map_data_from_options(
options
)
# output directory check
if isinstance(options.output_dir, str) and options.output_dir != ".":
if exists(options.output_dir):
output_dir = options.output_dir
else:
try:
create_dir(options.output_dir, False)
output_dir = options.output_dir
except (ValueError):
option_parser.error("Could not create output directory.")
exit(0)
else:
output_dir = get_random_directory_name()
# Generate the plots and html text
ymax = options.ymax
suppress_webpage = options.suppress_html_output
html_output = make_averages(
prefs, data, background_color, label_color, rares, output_dir, resolution, imagetype, ymax, suppress_webpage
)
if html_output:
# Write the html file.
outfile = open(path.join(output_dir, "rarefaction_plots.html"), "w")
outfile.write(html_output)
outfile.close()
