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Daniel Blankenberg
87eebd3206
These changes should only affect output when an input block has a species appearing more than once, with the exception being the MAF to multiple FASTA blocks converters: the FASTA headers have been revised to included the sequence index for a species in a block as well as the block index. A new tool "Split MAF Blocks by Species" has been added that will split MAF blocks into the complete combination of multiple blocks when a species appears more than once.
37 lines
1.1 KiB
Python
37 lines
1.1 KiB
Python
#!/usr/bin/env python
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#Dan Blankenberg
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"""
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Removes blocks that fall outside of specified size range.
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"""
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import sys
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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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assert sys.version_info[:2] >= ( 2, 4 )
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def __main__():
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input_maf_filename = sys.argv[1].strip()
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output_filename1 = sys.argv[2].strip()
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min_size = int( sys.argv[3].strip() )
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max_size = int( sys.argv[4].strip() )
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if max_size < 1: max_size = sys.maxint
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maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
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try:
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maf_reader = bx.align.maf.Reader( open( input_maf_filename, 'r' ) )
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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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blocks_kept = 0
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i = 0
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for i, m in enumerate( maf_reader ):
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if min_size <= m.text_size <= max_size:
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maf_writer.write( m )
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blocks_kept += 1
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print 'Kept %s of %s blocks (%.2f%%).' % ( blocks_kept, i + 1, float( blocks_kept ) / float( i + 1 ) * 100.0 )
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if __name__ == "__main__": __main__()
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