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()