1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d88ca4e4646c/ changeset: d88ca4e4646c user: jgoecks date: 2012-05-22 01:08:37 summary: Summary tree code tending: add todos and comments, remove version. affected #: 1 file
diff -r bdb5318e6d30cf78e7ab40205779909af22c45b6 -r d88ca4e4646c6bd3e601bd8f37fcb813385b3b45 lib/galaxy/visualization/tracks/summary.py --- a/lib/galaxy/visualization/tracks/summary.py +++ b/lib/galaxy/visualization/tracks/summary.py @@ -1,18 +1,17 @@ ''' -Summary tree data structure for aggregation - -10/20/2010: Changed version to 2 as we no longer look at bottom level, for better performance +Summary tree data structure for feature aggregation across large genomic regions. '''
import sys, os import cPickle
-VERSION = 2 +# TODO: What are the performance implications of setting min level to 1? Data +# structure size and/or query speed? It would be nice to have level 1 data +# so that client does not have to compute it. MIN_LEVEL = 2
class SummaryTree: def __init__( self, block_size, levels, draw_cutoff, detail_cutoff ): - self.version = VERSION self.chrom_blocks = {} self.levels = levels self.draw_cutoff = draw_cutoff @@ -26,20 +25,22 @@
def insert_range( self, chrom, start, end ): """ Inserts a feature at chrom:start-end into the tree. """ + + # Get or set up chrom blocks. if chrom in self.chrom_blocks: blocks = self.chrom_blocks[ chrom ] else: blocks = self.chrom_blocks[ chrom ] = {} self.chrom_stats[ chrom ] = {} - for level in range( MIN_LEVEL, self.levels+1 ): + for level in range( MIN_LEVEL, self.levels + 1 ): blocks[ level ] = {}
- - for level in range( MIN_LEVEL, self.levels+1 ): + # Insert feature into all matching blocks at all levels. + for level in range( MIN_LEVEL, self.levels + 1 ): block_level = blocks[ level ] starting_block = self.find_block( start, level ) ending_block = self.find_block( end, level ) - for block in range( starting_block, ending_block+1 ): + for block in range( starting_block, ending_block + 1 ): if block in block_level: block_level[ block ] += 1 else: @@ -47,6 +48,10 @@
def finish( self ): """ Checks for cutoff and only stores levels above it """ + + # TODO: not storing all counts is lossy. To fix, store all counts + # and then dynamically set draw/detail level either on load or + # use cutoffs in query function. for chrom, blocks in self.chrom_blocks.iteritems(): cur_best = 999 for level in range( self.levels, MIN_LEVEL-1, -1 ): @@ -75,11 +80,11 @@ elif "draw_level" in stats and level <= stats[ "draw_level" ]: return "draw" blocks = self.chrom_blocks[ chrom ] - results = [ ] + results = [] multiplier = self.block_size ** level starting_block = self.find_block( start, level ) ending_block = self.find_block( end, level ) - for block in range( starting_block, ending_block+1 ): + for block in range( starting_block, ending_block + 1 ): if block in blocks[ level ]: results.append( ( block * multiplier, blocks[ level ][ block ] ) ) return results
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.