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

"""
Tests for `bx.binned_array`.
"""

from numpy import *
from binned_array import *

random = random.random
 
# Bigger values take longer, but excercise more bins
CHUNK_SIZE_RANDOM=945
CHUNK_SIZE_ZEROS=897
##CHUNK_SIZE_RANDOM=9456
##CHUNK_SIZE_ZEROS=8972

source = target = None

def setup():
    global source
    global target
    source = []
    for i in range( 13 ):
        if random() < 0.5:
            source = concatenate( ( source, random( CHUNK_SIZE_RANDOM ) ) )
        else:
            source = concatenate( ( source, zeros( CHUNK_SIZE_ZEROS, 'f' ) ) )
    source = source.astype( 'f' )
    # Set on target
    target = BinnedArray( 128, NaN, len( source ) )
    for i in range( len( source ) ):
        # if not isNaN( source[i] ):
            target[i] = source[i]
    return source, target

def test_simple():
    # Verify
    for i in range( len( source ) ):
        assert source[i] == target[i], "No match, index: %d, source: %f, target: %f, len( source ): %d" % ( i, source[i], target[i], len( source ) )
    # Verify with slices
    for i in range( 10 ):
        a = int( random() * len( source ) )
        b = int( random() * len( source ) )
        if b < a: a, b = b, a
        assert allclose( source[a:b], target[a:b] ), "No match, index: %d:%d, source: %s, target: %s" % \
            ( a, b, ",".join( map( str, source[a:a+10] ) ), ",".join( map( str, target[a:a+10] ) ) )
 
def test_file():
    # With a file (zlib)
    target.to_file( open( "/tmp/foo", "w" ) )
    target2 = FileBinnedArray( open( "/tmp/foo" ) )
    for i in range( len( source ) ):
        assert source[i] == target2[i], "No match, index: %d, source: %d, target: %d" % ( i, source[i], target2[i] )
    # Verify with slices
    target2 = FileBinnedArray( open( "/tmp/foo" ) )
    for i in range( 10 ):
        a = int( random() * len( source ) )
        b = int( random() * len( source ) )
        if b < a: a, b = b, a
        assert allclose( source[a:b], target[a:b] ), "No match, index: %d:%d, source: %s, target: %s" % \
            ( a, b, ",".join( map( str, source[a:a+10] ) ), ",".join( map( str, target2[a:a+10] ) ) )
            
def test_file_lzo():
    # With a file (lzo)
    target.to_file( open( "/tmp/foo3", "w" ), comp_type="lzo" )
    target3 = FileBinnedArray( open( "/tmp/foo3" ) )
    # Verify
    for i in range( len( source ) ):
        assert source[i] == target3[i], "No match, index: %d, source: %d, target: %d" % ( i, source[i], target3[i] )
    # Verify with slices
    target3 = FileBinnedArray( open( "/tmp/foo3" ) )
    for i in range( 10 ):
        a = int( random() * len( source ) )
        b = int( random() * len( source ) )
        if b < a: a, b = b, a
        assert allclose( source[a:b], target3[a:b] ), "No match, index: %d:%d, source: %s, target: %s" % \
            ( a, b, ",".join( map( str, source[a:a+10] ) ), ",".join( map( str, target3[a:a+10] ) ) )
            
def test_binned_array_writer():
    # Test with ba writer
    o = open( "/tmp/foo4", "w" )
    w = BinnedArrayWriter( o, 128, comp_type='lzo' )
    for val in source:
        w.write( val )
    w.finish()
    o.close()
    # Verify
    target4 = FileBinnedArray( open( "/tmp/foo4" ) )
    for i in range( len( source ) ):
        assert allclose( source[i], target4[i] ), "No match, index: %d, source: %d, target: %d" % ( i, source[i], target4[i] )