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

リビジョン 3, 1.6 KB (コミッタ: kohda, 14 年 前)

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

行番号 
1import sys
2import twobit
3import random
4
5def quick_fasta_iter( f ):
6    current_header = None
7    current_sequence = []
8    for line in f:
9        if line.startswith( "#" ):
10            continue
11        if line.startswith( ">" ):
12            if current_sequence:
13                ## print current_header, "".join( current_sequence )
14                yield current_header, "".join( current_sequence )
15                current_sequence = []
16            current_header = line.strip()[1:]
17        else:
18            current_sequence.append( "".join( line.split() ) )
19    if current_sequence:
20        yield current_header, "".join( current_sequence )
21        current_sequence = []
22
23def test():
24    """
25    Nose test generator
26    """
27    for t in "test", "testN", "testMask":
28        test_fa = "test_data/seq_tests/%s.fa" % t
29        test_twobit = "test_data/seq_tests/%s.2bit" % t
30        yield check_random_subseq_matches, test_fa, test_twobit
31
32def check_random_subseq_matches( test_fa, test_twobit ):
33    # Load Fasta data
34    expected = {}
35    for h, s in quick_fasta_iter( open( test_fa ) ):
36        expected[h] = s
37    # Open 2bit
38    t = twobit.TwoBitFile( open( test_twobit ) )
39    for k, s in expected.iteritems():
40        assert k in t.index
41        # assert t.index[k].size == len(s)
42        length = len(s)
43        for i in range( 100 ):
44            start = random.randint( 0, length-2 )
45            end = random.randint( start+1, length )
46            assert t[k][start:end] == s[start:end], \
47                "seq: %s, start: %d, end: %d\nExpected:\n%s\nActual:\n%s\n" % ( k, start, end, s[start:end], t.get( k, start, end ) )
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