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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.
47 lines
1.7 KiB
Python
47 lines
1.7 KiB
Python
#!/usr/bin/env python
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#Dan Blankenberg
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"""
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Reads a list of block numbers and a maf. Produces a new maf containing the
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blocks specified by number.
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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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from galaxy.tools.util import maf_utilities
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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_block_filename = sys.argv[1].strip()
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input_maf_filename = sys.argv[2].strip()
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output_filename1 = sys.argv[3].strip()
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block_col = int( sys.argv[4].strip() ) - 1
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if block_col < 0:
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print >> sys.stderr, "Invalid column specified"
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sys.exit(0)
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species = maf_utilities.parse_species_option( sys.argv[5].strip() )
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maf_writer = bx.align.maf.Writer( open( output_filename1, 'w' ) )
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#we want to maintain order of block file and write blocks as many times as they are listed
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failed_lines = []
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for ctr, line in enumerate( open( input_block_filename, 'r' ) ):
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try:
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block_wanted = int( line.split( "\t" )[block_col].strip() )
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except:
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failed_lines.append( str( ctr ) )
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continue
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try:
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for count, block in enumerate( bx.align.maf.Reader( open( input_maf_filename, 'r' ) ) ):
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if count == block_wanted:
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if species:
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block = block.limit_to_species( species )
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maf_writer.write( block )
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break
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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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if len( failed_lines ) > 0: print "Failed to extract from %i lines (%s)." % ( len( failed_lines ), ",".join( failed_lines ) )
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if __name__ == "__main__": __main__()
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