opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Cleanup for previous commit, 565476ce4f03, mainly to further comment and simplify code and avoid going to index multiple times.

Browse Source
This commit is contained in:
Jeremy Goecks
2012-08-15 18:09:48 -04:00
parent 5dda060e33
commit 54b1f8097a
1 changed files with 17 additions and 14 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/visualization/tracks/data_providers.py
+17 -14
View File
@@ -985,28 +985,31 @@ class BBIDataProvider( TracksDataProvider ):
# To do this, need to increase end to next base and request number of points.
num_points = end - start + 1
end += 1
result = summarize_region( bbi, chrom, start, end, num_points )
else:
#
# The goal is to sample the region between start and end uniformly
# using N data points. The challenge is that the size of sampled
# using ~N data points. The challenge is that the size of sampled
# intervals rarely is full bases, so sampling using N points will
# leave the end of the region unsampled. To recitify this, samples
# beyond N are taken at the end of the interval.
# leave the end of the region unsampled due to remainders for each
# interval. To recitify this, a new N is calculated based on the
# step size that covers as much of the region as possible.
#
# However, this still leaves some of the region unsampled. This
# could be addressed by repeatedly sampling remainder using a
# smaller and smaller step_size, but that would require iteratively
# going to BBI, which could be time consuming.
#
# Do initial summary.
# Start with N samples.
num_points = N
result = summarize_region( bbi, chrom, start, end, num_points )
# Do summary of remaining part of region.
step_size = ( end - start ) / num_points
new_start = start + step_size * num_points
new_num_points = min( ( end - new_start ) / step_size, end - start )
if new_num_points is not 0:
result.extend( summarize_region( bbi, chrom, new_start, end, new_num_points ) )
#TODO: progressively reduce step_size to generate more datapoints.
# Add additional points to sample in the remainder not covered by
# the initial N samples.
remainder_start = start + step_size * num_points
additional_points = ( end - remainder_start ) / step_size
num_points += additional_points
result = summarize_region( bbi, chrom, start, end, num_points )
# Cleanup and return.
f.close()