Mercurial > repos > xuebing > sharplabtool
comparison tools/maf/maf_limit_size.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 #!/usr/bin/env python | |
| 2 #Dan Blankenberg | |
| 3 """ | |
| 4 Removes blocks that fall outside of specified size range. | |
| 5 """ | |
| 6 | |
| 7 import sys | |
| 8 from galaxy import eggs | |
| 9 import pkg_resources; pkg_resources.require( "bx-python" ) | |
| 10 import bx.align.maf | |
| 11 | |
| 12 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 13 | |
| 14 def __main__(): | |
| 15 | |
| 16 input_maf_filename = sys.argv[1].strip() | |
| 17 output_filename1 = sys.argv[2].strip() | |
| 18 min_size = int( sys.argv[3].strip() ) | |
| 19 max_size = int( sys.argv[4].strip() ) | |
| 20 if max_size < 1: max_size = sys.maxint | |
| 21 maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) ) | |
| 22 try: | |
| 23 maf_reader = bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) | |
| 24 except: | |
| 25 print >>sys.stderr, "Your MAF file appears to be malformed." | |
| 26 sys.exit() | |
| 27 | |
| 28 blocks_kept = 0 | |
| 29 i = 0 | |
| 30 for i, m in enumerate( maf_reader ): | |
| 31 if min_size <= m.text_size <= max_size: | |
| 32 maf_writer.write( m ) | |
| 33 blocks_kept += 1 | |
| 34 print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 ) | |
| 35 | |
| 36 if __name__ == "__main__": __main__() |