root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/bx/binned_array_tests.py

リビジョン 3, 3.3 KB (コミッタ: kohda, 14 年 前)

Install Unix tools  http://hannonlab.cshl.edu/galaxy_unix_tools/galaxy.html

行番号 
1"""
2Tests for `bx.binned_array`.
3"""
4
5from numpy import *
6from binned_array import *
7
8random = random.random
9 
10# Bigger values take longer, but excercise more bins
11CHUNK_SIZE_RANDOM=945
12CHUNK_SIZE_ZEROS=897
13##CHUNK_SIZE_RANDOM=9456
14##CHUNK_SIZE_ZEROS=8972
15
16source = target = None
17
18def setup():
19    global source
20    global target
21    source = []
22    for i in range( 13 ):
23        if random() < 0.5:
24            source = concatenate( ( source, random( CHUNK_SIZE_RANDOM ) ) )
25        else:
26            source = concatenate( ( source, zeros( CHUNK_SIZE_ZEROS, 'f' ) ) )
27    source = source.astype( 'f' )
28    # Set on target
29    target = BinnedArray( 128, NaN, len( source ) )
30    for i in range( len( source ) ):
31        # if not isNaN( source[i] ):
32            target[i] = source[i]
33    return source, target
34
35def test_simple():
36    # Verify
37    for i in range( len( source ) ):
38        assert source[i] == target[i], "No match, index: %d, source: %f, target: %f, len( source ): %d" % ( i, source[i], target[i], len( source ) )
39    # Verify with slices
40    for i in range( 10 ):
41        a = int( random() * len( source ) )
42        b = int( random() * len( source ) )
43        if b < a: a, b = b, a
44        assert allclose( source[a:b], target[a:b] ), "No match, index: %d:%d, source: %s, target: %s" % \
45            ( a, b, ",".join( map( str, source[a:a+10] ) ), ",".join( map( str, target[a:a+10] ) ) )
46 
47def test_file():
48    # With a file (zlib)
49    target.to_file( open( "/tmp/foo", "w" ) )
50    target2 = FileBinnedArray( open( "/tmp/foo" ) )
51    for i in range( len( source ) ):
52        assert source[i] == target2[i], "No match, index: %d, source: %d, target: %d" % ( i, source[i], target2[i] )
53    # Verify with slices
54    target2 = FileBinnedArray( open( "/tmp/foo" ) )
55    for i in range( 10 ):
56        a = int( random() * len( source ) )
57        b = int( random() * len( source ) )
58        if b < a: a, b = b, a
59        assert allclose( source[a:b], target[a:b] ), "No match, index: %d:%d, source: %s, target: %s" % \
60            ( a, b, ",".join( map( str, source[a:a+10] ) ), ",".join( map( str, target2[a:a+10] ) ) )
61           
62def test_file_lzo():
63    # With a file (lzo)
64    target.to_file( open( "/tmp/foo3", "w" ), comp_type="lzo" )
65    target3 = FileBinnedArray( open( "/tmp/foo3" ) )
66    # Verify
67    for i in range( len( source ) ):
68        assert source[i] == target3[i], "No match, index: %d, source: %d, target: %d" % ( i, source[i], target3[i] )
69    # Verify with slices
70    target3 = FileBinnedArray( open( "/tmp/foo3" ) )
71    for i in range( 10 ):
72        a = int( random() * len( source ) )
73        b = int( random() * len( source ) )
74        if b < a: a, b = b, a
75        assert allclose( source[a:b], target3[a:b] ), "No match, index: %d:%d, source: %s, target: %s" % \
76            ( a, b, ",".join( map( str, source[a:a+10] ) ), ",".join( map( str, target3[a:a+10] ) ) )
77           
78def test_binned_array_writer():
79    # Test with ba writer
80    o = open( "/tmp/foo4", "w" )
81    w = BinnedArrayWriter( o, 128, comp_type='lzo' )
82    for val in source:
83        w.write( val )
84    w.finish()
85    o.close()
86    # Verify
87    target4 = FileBinnedArray( open( "/tmp/foo4" ) )
88    for i in range( len( source ) ):
89        assert allclose( source[i], target4[i] ), "No match, index: %d, source: %d, target: %d" % ( i, source[i], target4[i] )
90           
91           
92           
93           
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。