Example #1
0
def test_my_wil_rank_sum_gtr():
     """nosetest for utils.my_wil_rank_sum_gtr"""

     # test gtr dist
     vals = []
     for x in xrange(1000):
          vals.append(random.randint(0, 10000))
     vals.sort()
     low_vals = vals[0:300]
     high_vals = vals[800:]

     pval = utils.my_wil_rank_sum_gtr(high_vals, low_vals,
                                      vals)
     nose.tools.assert_true(pval < float(.01))

     # test eq dist
     low_vals = []
     for x in xrange(300):
          low_vals.append( vals[random.randint(0,999)] )
     high_vals = []
     for x in xrange(300):
          high_vals.append( vals[random.randint(0,999)] )

     pval = utils.my_wil_rank_sum_gtr(high_vals, low_vals,
                                      vals)
     nose.tools.assert_true(pval > float(.05),
                            'pval was significant, but should not be '
                            + str(pval))
Example #2
0
   human_all_vals) = plot_fore_control(outfile, protein, 
                                       human_fore, human_control, 
                                       human_all,
                                       human_host_freqs, 
                                       chicken_host_freqs)
 outfile = os.path.join(dir, 'chicken_' + protein + '.png')
 (chicken_fore_vals,
  chicken_control_vals,
  chicken_all_vals)  = plot_fore_control(outfile, protein, 
                                         chicken_fore, 
                                         chicken_control, 
                                         chicken_all,
                                         chicken_host_freqs, 
                                         human_host_freqs)
  human_control_pval = utils.my_wil_rank_sum_gtr(human_fore_vals,
                                                 human_control_vals,
                                                 human_all_vals)
  chicken_control_pval = utils.my_wil_rank_sum_gtr(chicken_fore_vals,
                                                 chicken_control_vals,
                                                 chicken_all_vals)
 if protein in ('polymerase PB1', 'neuraminidase', 'polymerase PB2',
                'nonstructural protein 2', 'polymerase PA',
                'matrix protein 2'):
     human_pval = 'fore gtr ' + str(len(human_fore_vals)) + ' ' + str(len(human_control_vals) )+ ' ' + str(utils_stats.wilcox_gtr(human_fore_vals, human_control_vals))
     p = utils_stats.wilcox_gtr(chicken_fore_vals, chicken_control_vals)
     print 'pval', p, 'yo'
     chicken_pval = 'fore gtr ' + str(len(chicken_fore_vals)) + ' ' + str(len(chicken_control_vals)) + ' ' + str(p)
 else:
     human_pval = 'ctrl gtr ' + str(len(human_control_vals)) + ' ' + str(len(human_fore_vals)) + ' ' + str(utils_stats.wilcox_gtr(human_control_vals, human_fore_vals))
     chicken_pval = 'ctrl gtr ' + str(len(chicken_control_vals)) + ' ' + str(len(chicken_fore_vals)) + ' ' + str(utils_stats.wilcox_gtr(chicken_control_vals, chicken_fore_vals))
 print 'human pval', protein, human_pval