root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/bx/misc/seekbzip2_tests.py

リビジョン 3, 2.5 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.misc.seekbzip2`.
3"""
4
5import tempfile
6import commands
7import os
8import random
9from itertools import *
10
11import seekbzip2
12import bz2
13
14F=None
15T=None
16
17#F="/Users/james/work/seek-bzip2/test_random.dat.bz2"
18#T="/Users/james/cache/hg18/align/multiz28way/chr10.maf.bz2"
19
20#F=/depot/data1/cache/human/hg18/align/multiz28way/chr1.maf.bz2
21
22import sys
23
24if F and os.path.exists( F ):
25
26    def test_linear_reading():
27        raw_data = bz2.BZ2File( F ).read()
28        f = seekbzip2.SeekableBzip2File( F, F + "t" )
29        chunk = 1221
30        pos = 0
31        for i in range( ( len(raw_data) // chunk ) + 1 ):
32            a = raw_data[pos:pos+chunk]
33            b = f.read( chunk )
34            assert a == b
35            pos += chunk
36            assert f.tell() == min( pos, len(raw_data) )
37        f.close()
38       
39    def test_random_seeking():
40        raw_data = bz2.BZ2File( F ).read()
41        f = seekbzip2.SeekableBzip2File( F, F + "t" )
42        for i in range( 10 ):
43            seek_to = random.randrange( len( raw_data ) - 100 )
44            chunk = random.randrange( 10, 20 )
45
46            f.seek( seek_to )
47            a = f.read( chunk )
48            b = raw_data[ seek_to : seek_to + chunk ]
49       
50            assert a == b, "'%s' != '%s' on %dth attempt" % ( a.encode("hex"), b.encode("hex"), i )
51
52            assert f.tell() == min( seek_to + chunk, len(raw_data) )
53        f.close()
54           
55if T and os.path.exists( T ):
56       
57    def test_text_reading():
58        #raw_data = bz2.BZ2File( T ).read()
59        #raw_lines = raw_data.split( "\n" )
60        raw_file = bz2.BZ2File( T )
61        f = seekbzip2.SeekableBzip2File( T, T + "t" )
62        pos = 0
63        for i, ( line, raw_line ) in enumerate( izip( f, raw_file ) ):
64            assert line == raw_line, "%d: %r != %r" % ( i, line.rstrip( "\n" ), raw_line )
65            pos += len( line )
66            ftell = f.tell()
67            assert ftell == pos, "%d != %d" % ( ftell, pos )
68        f.close()
69       
70 
71    def test_text_reading_2():
72        raw_data = bz2.BZ2File( T ).read()
73        f = seekbzip2.SeekableBzip2File( T, T + "t" )
74        raw_lines = raw_data.split( "\n" )
75        pos = 0
76        i = 0
77        while 1:
78            line = f.readline()
79            if line == "": break
80            assert line.rstrip( "\r\n" ) == raw_lines[i], "%r != %r" % ( line.rstrip( "\r\n" ), raw_lines[i] )
81            pos += len( line )
82            ftell = f.tell()
83            assert ftell == pos, "%d != %d" % ( ftell, pos ) 
84            i += 1   
85        f.close()
86       
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。