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36 lines
976 B
Python
36 lines
976 B
Python
#!/usr/bin/env python
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# Dan Blankenberg
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"""
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Removes blocks that fall outside of specified size range.
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"""
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import sys
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import bx.align.maf
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def __main__():
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input_maf_filename = sys.argv[1].strip()
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output_filename1 = sys.argv[2].strip()
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min_size = int( sys.argv[3].strip() )
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max_size = int( sys.argv[4].strip() )
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if max_size < 1:
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max_size = sys.maxint
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maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
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try:
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maf_reader = bx.align.maf.Reader( open( input_maf_filename, 'r' ) )
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except:
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print >>sys.stderr, "Your MAF file appears to be malformed."
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sys.exit()
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blocks_kept = 0
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i = 0
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for i, m in enumerate( maf_reader ):
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if min_size <= m.text_size <= max_size:
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maf_writer.write( m )
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blocks_kept += 1
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print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 )
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if __name__ == "__main__":
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__main__()
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