Mercurial > repos > xuebing > sharplabtool
diff tools/maf/maf_limit_size.py @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/maf/maf_limit_size.py Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,36 @@ +#!/usr/bin/env python +#Dan Blankenberg +""" +Removes blocks that fall outside of specified size range. +""" + +import sys +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +import bx.align.maf + +assert sys.version_info[:2] >= ( 2, 4 ) + +def __main__(): + + input_maf_filename = sys.argv[1].strip() + output_filename1 = sys.argv[2].strip() + min_size = int( sys.argv[3].strip() ) + max_size = int( sys.argv[4].strip() ) + if max_size < 1: max_size = sys.maxint + maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) ) + try: + maf_reader = bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) + except: + print >>sys.stderr, "Your MAF file appears to be malformed." + sys.exit() + + blocks_kept = 0 + i = 0 + for i, m in enumerate( maf_reader ): + if min_size <= m.text_size <= max_size: + maf_writer.write( m ) + blocks_kept += 1 + print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 ) + +if __name__ == "__main__": __main__()