def test_matrix_stats1(self):
""" matrix_stats should match mean, median, stdev calc'd by hand"""
headers_list = [['a', 'c', 'b'], ['a', 'c', 'b']]
d1 = numpy.array([[0, .2, .9], [.2, 0, .8], [.9, .8, 0]], 'float')
d2 = numpy.array([[0, .3, 1.1], [.3, 0, .8], [1.1, .8, 0]], 'float')
distmats_list = [d1, d2]
exp_mean = numpy.array([[0, .25, 1.0], [.25, 0, .8], [1.0, .8, 0]],
'float')
exp_median = numpy.array([[0, .25, 1.0], [.25, 0, .8], [1.0, .8, 0]],
'float')
exp_std = numpy.array([[0, .05, .1], [.05, 0, 0], [.1, 0, 0]], 'float')
results = matrix_stats(headers_list, distmats_list)
self.assertFloatEqual(results[1:], [exp_mean, exp_median, exp_std])
self.assertEqual(results[0], ['a', 'c', 'b'])
def test_matrix_stats1(self):
""" matrix_stats should match mean, median, stdev calc'd by hand"""
headers_list = [['a','c','b'],['a','c','b']]
d1 = numpy.array([ [ 0,.2,.9],
[.2,0,.8],
[.9,.8,0]],'float')
d2 = numpy.array([ [ 0,.3,1.1],
[.3,0,.8],
[1.1,.8,0]],'float')
distmats_list = [d1,d2]
exp_mean = numpy.array([ [ 0,.25,1.0],
[.25,0,.8],
[1.0,.8,0]],'float')
exp_median = numpy.array([ [ 0,.25,1.0],
[.25,0,.8],
[1.0,.8,0]],'float')
exp_std = numpy.array([ [ 0,.05,.1],
[.05,0,0],
[.1,0,0]],'float')
results = matrix_stats(headers_list, distmats_list)
self.assertFloatEqual(results[1:], [exp_mean,exp_median,exp_std])
self.assertEqual(results[0],['a','c','b'])
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
indir = opts.input_dir
outdir = opts.output_dir
if not os.path.exists(outdir):
os.makedirs(outdir)
# input
file_names = os.listdir(indir)
file_names = [fname for fname in file_names if not fname.startswith('.')]
distmats = []
headers_list = []
for fname in file_names:
f = open(os.path.join(indir, fname), 'U')
headers, data = parse_distmat(f)
f.close()
distmats.append(data)
headers_list.append(headers)
# calcs
headers, means, medians, stdevs = matrix_stats(headers_list, distmats)
# output
f = open(os.path.join(outdir, 'means.txt'), 'w')
f.write(format_distance_matrix(headers, means))
f.close()
f = open(os.path.join(outdir, 'medians.txt'), 'w')
f.write(format_distance_matrix(headers, medians))
f.close()
f = open(os.path.join(outdir, 'stdevs.txt'), 'w')
f.write(format_distance_matrix(headers, stdevs))
f.close()
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
indir = opts.input_dir
outdir = opts.output_dir
if not os.path.exists(outdir):
os.makedirs(outdir)
#input
file_names = os.listdir(indir)
file_names = [fname for fname in file_names if not fname.startswith('.')]
distmats = []
headers_list = []
for fname in file_names:
f = open(os.path.join(indir,fname), 'U')
headers, data = parse_distmat(f)
f.close()
distmats.append(data)
headers_list.append(headers)
#calcs
headers, means, medians, stdevs = matrix_stats(headers_list, distmats)
#output
f = open(os.path.join(outdir,'means.txt'), 'w')
f.write(format_distance_matrix(headers,means))
f.close()
f = open(os.path.join(outdir,'medians.txt'), 'w')
f.write(format_distance_matrix(headers,medians))
f.close()
f = open(os.path.join(outdir,'stdevs.txt'), 'w')
f.write(format_distance_matrix(headers,stdevs))
f.close()
