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Daniel Blankenberg
5b1552ffa8
Add new bx-python eggs. Reorganize all MAF tools into a unified directory, and update tool_conf. Remember to update tool_conf.xml from one of the samples (tool_conf.xml.sample or tool_conf.xml.main).
35 lines
994 B
Python
35 lines
994 B
Python
#!/usr/bin/env python2.4
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"""
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Reads a MAF file. Produces a MAF file containing
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the reverse complement for each block in the source file.
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usage: %prog input_maf_file output_maf_file
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"""
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#Dan Blankenberg
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import pkg_resources; pkg_resources.require( "bx-python" )
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import bx.align.maf
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import sys
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def __main__():
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#Parse Command Line
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input_file = sys.argv.pop( 1 )
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output_file = sys.argv.pop( 1 )
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try:
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maf_writer = bx.align.maf.Writer( open( output_file, 'w' ) )
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except:
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print sys.stderr, "Unable to open output file"
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sys.exit()
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try:
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count = 0
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for count, maf in enumerate( bx.align.maf.Reader( open( input_file ) ) ):
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maf_writer.write( maf.reverse_complement() )
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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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print "%i regions were reverse complemented." % count
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maf_writer.close()
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if __name__ == "__main__": __main__()
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