[2] | 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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