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1 #!/usr/bin/env python
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2
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3 """
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4 Reads a MAF file. Produces a MAF file containing
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5 the reverse complement for each block in the source file.
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6
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7 usage: %prog input_maf_file output_maf_file
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8 """
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9 #Dan Blankenberg
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10 from galaxy import eggs
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11 import pkg_resources; pkg_resources.require( "bx-python" )
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12 import bx.align.maf
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13 from galaxy.tools.util import maf_utilities
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14 import sys
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15
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16 assert sys.version_info[:2] >= ( 2, 4 )
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17
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18 def __main__():
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19 #Parse Command Line
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20 input_file = sys.argv.pop( 1 )
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21 output_file = sys.argv.pop( 1 )
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22 species = maf_utilities.parse_species_option( sys.argv.pop( 1 ) )
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23
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24 try:
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25 maf_writer = bx.align.maf.Writer( open( output_file, 'w' ) )
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26 except:
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27 print sys.stderr, "Unable to open output file"
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28 sys.exit()
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29 try:
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30 count = 0
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31 for count, maf in enumerate( bx.align.maf.Reader( open( input_file ) ) ):
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32 maf = maf.reverse_complement()
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33 if species:
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34 maf = maf.limit_to_species( species )
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35 maf_writer.write( maf )
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36 except:
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37 print >>sys.stderr, "Your MAF file appears to be malformed."
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38 sys.exit()
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39 print "%i regions were reverse complemented." % count
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40 maf_writer.close()
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41
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42 if __name__ == "__main__": __main__()
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