bx-python / scripts / maf_randomize.py

#!/usr/bin/env python

Randomize the order of blocks in a MAF file. If `sample_size` is specified,
that many random blocks will be kept from the original maf

usage: %prog [sample_size] < maf > maf

import sys

import sys, random
from bx.align import maf
from math import *
from optparse import OptionParser

def __main__():

    #if len( sys.argv ) > 1: fraction = float( sys.argv[1] )
    if len( sys.argv ) > 1: sample_size = int( sys.argv[1] )

    maf_reader = maf.Reader( sys.stdin )
    maf_writer = maf.Writer( sys.stdout )

    mafs = list( maf_reader )

    # for m in maf_reader: mafs.append( m )

    random.shuffle( mafs )

    if not sample_size: sample_size = len( mafs )

    for i in range( 0, sample_size ): maf_writer.write( mafs[ i ] )
if __name__ == "__main__": __main__()
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