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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3 """
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4 Removes blocks that fall outside of specified size range.
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5 """
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6
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7 import sys
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8 from galaxy import eggs
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9 import pkg_resources; pkg_resources.require( "bx-python" )
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10 import bx.align.maf
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11
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12 assert sys.version_info[:2] >= ( 2, 4 )
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13
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14 def __main__():
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15
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16 input_maf_filename = sys.argv[1].strip()
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17 output_filename1 = sys.argv[2].strip()
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18 min_size = int( sys.argv[3].strip() )
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19 max_size = int( sys.argv[4].strip() )
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20 if max_size < 1: max_size = sys.maxint
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21 maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
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22 try:
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23 maf_reader = bx.align.maf.Reader( open( input_maf_filename, 'r' ) )
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24 except:
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25 print >>sys.stderr, "Your MAF file appears to be malformed."
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26 sys.exit()
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27
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28 blocks_kept = 0
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29 i = 0
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30 for i, m in enumerate( maf_reader ):
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31 if min_size <= m.text_size <= max_size:
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32 maf_writer.write( m )
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33 blocks_kept += 1
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34 print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 )
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35
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36 if __name__ == "__main__": __main__()
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