1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2d937ad3e1b4/ changeset: 2d937ad3e1b4 user: jgoecks date: 2012-08-19 00:00:31 summary: Streamline creation of stats for BBI tracks data provider. affected #: 1 file diff -r d62d3c23a61377f3d7928b56e7af346d502aac73 -r 2d937ad3e1b47492f64fa0b9c668529a735118e8 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -968,29 +968,32 @@ # which we use converted_dataset f, bbi = self._get_dataset() - # If the stats kwarg was provide, we compute overall summary data for the - # range defined by start and end but no reduced data. This is currently - # used by client to determine the default range. + # If stats requested, compute overall summary data for the range + # start:endbut no reduced data. This is currently used by client + # to determine the default range. if 'stats' in kwargs: summary = bbi.summarize( chrom, start, end, 1 ) f.close() - if summary is None: - return None - else: + + min = 0 + max = 0 + mean = 0 + sd = 0 + if summary is not None: # Does the summary contain any defined values? valid_count = summary.valid_count[0] - if summary.valid_count < 1: - return None + if summary.valid_count > 0: + # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower + # bounds that contain ~95% of the data. + mean = summary.sum_data[0] / valid_count + var = summary.sum_squares[0] - mean + if valid_count > 1: + var /= valid_count - 1 + sd = numpy.sqrt( var ) + min = summary.min_val[0] + max = summary.max_val[0] - # Compute $\mu \pm 2\sigma$ to provide an estimate for upper and lower - # bounds that contain ~95% of the data. - mean = summary.sum_data[0] / valid_count - var = summary.sum_squares[0] - mean - if valid_count > 1: - var /= valid_count - 1 - sd = numpy.sqrt( var ) - - return dict( data=dict( min=summary.min_val[0], max=summary.max_val[0], mean=mean, sd=sd ) ) + return dict( data=dict( min=min, max=max, mean=mean, sd=sd ) ) # Sample from region using approximately this many samples. N = 1000 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.