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

リビジョン 3, 2.8 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"""
2Tools for fusing contiguous alignment blocks together.
3"""
4
5from itertools import *
6from copy import deepcopy
7
8def fuse_list( mafs ):
9    """
10    Try to fuse a list of blocks by progressively fusing each adjacent pair.
11    """
12    last = None
13    for m in mafs:
14        if last is None:
15            last = m
16        else:
17            fused = fuse( last, m )
18            if fused:
19                last = fused
20            else:
21                yield last
22                last = m
23    if last:
24        yield last
25
26def fuse( m1, m2 ):
27    """
28    Attempt to fuse two blocks. If they can be fused returns a new block,
29    otherwise returns None.
30     
31    Example:
32     
33    >>> import bx.align.maf
34     
35    >>> block1 = bx.align.maf.from_string( '''
36    ... a score=0.0
37    ... s hg18.chr10 52686 44 + 135374737 GTGCTAACTTACTGCTCCACAGAAAACATCAATTCTGCTCATGC
38    ... s panTro1.chrUn_random 208115356 44 - 240967748 GTGCTAACTGACTGCTCCAGAGAAAACATCAATTCTGTTCATGT
39    ... ''' )
40   
41    >>> block2 = bx.align.maf.from_string( '''
42    ... a score=0.0
43    ... s hg18.chr10 52730 69 + 135374737 GCAGGTACAATTCATCAAGAAAGGAATTACAACTTCAGAAATGTGTTCAAAATATATCCATACTTTGAC
44    ... s panTro1.chrUn_random 208115400 69 - 240967748 GCAGCTACTATTCATCAAGAAAGGGATTACAACTTCAGAAATGTGTTCAAAGTGTATCCATACTTTGAT
45    ... ''' )
46   
47    >>> fused = fuse( block1, block2 )
48   
49    >>> print fused
50    a score=0.0
51    s hg18.chr10 52686 113 + 135374737 GTGCTAACTTACTGCTCCACAGAAAACATCAATTCTGCTCATGCGCAGGTACAATTCATCAAGAAAGGAATTACAACTTCAGAAATGTGTTCAAAATATATCCATACTTTGAC
52    s panTro1.chrUn_random 208115356 113 - 240967748 GTGCTAACTGACTGCTCCAGAGAAAACATCAATTCTGTTCATGTGCAGCTACTATTCATCAAGAAAGGGATTACAACTTCAGAAATGTGTTCAAAGTGTATCCATACTTTGAT
53    <BLANKLINE>
54    """
55    # Check if the blocks are adjacent, return none if not.
56    if len( m1.components ) != len( m2.components ): return None
57    for c1, c2 in izip( m1.components, m2.components ):
58        if c1.src != c2.src: return None
59        if c1.strand != c2.strand: return None
60        if c1.end != c2.start: return None
61    # Try to fuse:
62    n = deepcopy( m1 )
63    for c1, c2 in izip( n.components, m2.components ):
64        c1.text += c2.text
65        c1.size += c2.size
66    n.text_size = len( n.components[0].text )
67    return n
68   
69class FusingAlignmentWriter( object ):
70    """
71    Wrapper for an alignment Writer which attempts to fuse adjacent blocks
72    """
73    def __init__( self, maf_writer ):
74        self.maf_writer = maf_writer
75        self.last = None
76    def write( self, m ):
77        if not self.last:
78            self.last = m
79        else:
80            fused = fuse( self.last, m )
81            if fused:
82                self.last = fused
83            else:
84                self.maf_writer.write( self.last )
85                self.last = m
86    def close( self ):
87        if self.last: self.maf_writer.write( self.last )
88        self.maf_writer.close()
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