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https://github.com/galaxyproject/galaxy.git
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Daniel Blankenberg
377c2427a7
Allow most MAF tools to allow limiting of output species. MAF tools which do not allow species limiting include Extract Pairwise MAF blocks, MAF Coverage stats, and Filter MAF blocks by Size. The functionality of Filter MAF blocks by Species and Filter MAF blocks by Size is now available in Filter MAF by specified attributes. Unfortunately tests are still not able to be written for the Filter MAF by specified attributes tool.
43 lines
1.2 KiB
Python
43 lines
1.2 KiB
Python
#!/usr/bin/env python
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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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from galaxy import eggs
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import pkg_resources; pkg_resources.require( "bx-python" )
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import bx.align.maf
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from galaxy.tools.util import maf_utilities
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import sys
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assert sys.version_info[:2] >= ( 2, 4 )
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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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species = maf_utilities.parse_species_option( 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 = maf.reverse_complement()
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if species:
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maf = maf.limit_to_species( species )
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maf_writer.write( maf )
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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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