root/galaxy-central/lib/galaxy/visualization/tracks/summary.py

リビジョン 2, 3.5 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1'''
22010, Kanwei Li
3Summary tree data structure for aggregation
4
510/20/2010: Changed version to 2 as we no longer look at bottom level, for better performance
6'''
7
8import sys, os
9import cPickle
10
11VERSION = 2
12MIN_LEVEL = 2
13
14class SummaryTree:
15    def __init__(self, block_size, levels, draw_cutoff, detail_cutoff):
16        self.version = VERSION
17        self.chrom_blocks = {}
18        self.levels = levels
19        self.draw_cutoff = draw_cutoff
20        self.detail_cutoff = detail_cutoff
21        self.block_size = block_size
22        self.chrom_stats = {}
23   
24    def find_block(self, num, level):
25        return (num / self.block_size ** level)
26       
27    def insert_range(self, chrom, start, end):
28        if chrom in self.chrom_blocks:
29            blocks = self.chrom_blocks[chrom]
30        else:
31            blocks = self.chrom_blocks[chrom] = {}
32            self.chrom_stats[chrom] = {}
33            for level in range(MIN_LEVEL, self.levels+1):
34                blocks[level] = {}
35           
36           
37        for level in range(MIN_LEVEL, self.levels+1):
38            block_level = blocks[level]
39            starting_block = self.find_block(start, level)
40            ending_block = self.find_block(end, level)
41            for block in range(starting_block, ending_block+1):
42                if block in block_level:
43                    block_level[block] += 1
44                else:
45                    block_level[block] = 1
46       
47    def finish(self):
48        ''' Checks for cutoff and only stores levels above it '''
49        for chrom, blocks in self.chrom_blocks.iteritems():
50            cur_best = 999
51            for level in range(self.levels, MIN_LEVEL-1, -1):
52                max_val = max(blocks[level].values())
53                if max_val < self.draw_cutoff:
54                    if "draw_level" not in self.chrom_stats[chrom]:
55                        self.chrom_stats[chrom]["draw_level"] = level
56                    elif max_val < self.detail_cutoff:
57                        self.chrom_stats[chrom]["detail_level"] = level
58                        break
59                else:
60                    self.chrom_stats[chrom][level] = {}
61                    self.chrom_stats[chrom][level]["delta"] = self.block_size ** level
62                    self.chrom_stats[chrom][level]["max"] = max_val
63                    self.chrom_stats[chrom][level]["avg"] = float(max_val) / len(blocks[level])
64                    cur_best = level
65           
66            self.chrom_blocks[chrom] = dict([ (key, value) for key, value in blocks.iteritems() if key >= cur_best ])
67       
68    def query(self, chrom, start, end, level):
69        if chrom in self.chrom_blocks:
70            stats = self.chrom_stats[chrom]
71            if "detail_level" in stats and level <= stats["detail_level"]:
72                return "detail"
73            elif "draw_level" in stats and level <= stats["draw_level"]:
74                return "draw"
75            blocks = self.chrom_blocks[chrom]
76            results = []
77            multiplier = self.block_size ** level
78            starting_block = self.find_block(start, level)
79            ending_block = self.find_block(end, level)
80            for block in range(starting_block, ending_block+1):
81                if block in blocks[level]:
82                    results.append( (block * multiplier, blocks[level][block]) )
83            return results
84           
85        return None
86       
87    def write(self, filename):
88        self.finish()
89        cPickle.dump(self, open(filename, 'wb'), 2)
90       
91def summary_tree_from_file(filename):
92    return cPickle.load(open(filename, "r"))
93   
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