root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/EGG-INFO/scripts/maf_chop.py

リビジョン 3, 1.5 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#!/usr/bin/python2.6
2
3"""
4Chops alignments in a MAF file to piece of a specified length. A random set of
5non overlapping chunks of exactly the specified chop length will be produced
6
7usage: %prog [options] < maf > maf
8  -l, --length: Chop to exactly this length in columns (default 100)
9"""
10
11import sys
12
13import sys, random
14import bx.align.maf
15from optparse import OptionParser
16
17def main():
18
19    # Parse command line arguments
20
21    parser = OptionParser()
22    parser.add_option( "-l", "--length", action="store", type="int", default=100, help="" )
23
24    ( options, args ) = parser.parse_args()
25
26    length = options.length
27    maf_reader = bx.align.maf.Reader( sys.stdin )
28    maf_writer = bx.align.maf.Writer( sys.stdout )
29
30    for m in maf_reader:
31        for chopped in chop( m, length ):
32            maf_writer.write( chopped )
33
34def chop( m, length ):
35    maf_length = m.text_size
36    chunk_count = maf_length // length
37    lost_bases = maf_length % length
38    skip_amounts = [0] * ( chunk_count + 1 )
39    for i in range( 0, lost_bases ): skip_amounts[ random.randrange( 0, chunk_count + 1 ) ] += 1
40    start = 0
41    rval = []
42    for i in range( 0, chunk_count ):
43        start += skip_amounts[ i ]
44        n = m.slice( start, start + length )
45        if check_len( n ): rval.append( m.slice( start, start + length ) )
46        start += length
47    return rval
48
49def check_len( a ):
50    for c in a.components:
51        if c.size == 0: return False
52    return True
53   
54
55if __name__ == "__main__": main()
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