@files( (PARAMS["rates_alignment"], 
         PARAMS["genes"]), 
        "alignment_filtered.psl.gz" )
def buildFilteredAlignment( infiles, outfile ):
    infile_alignment, infile_genes = infiles
    to_cluster = True
    statement = '''gunzip 
	< %(infile_alignment)s 
	| python %(scriptsdir)s/psl2psl.py 
		--method=filter-remove 
		--filter-query=<(gunzip < %(infile_genes)s)
		--log=%(outfile)s.log 
        > %(outfile)s '''

    P.run()
build a genomic alignment without exons
dataset/ETHPy150Open CGATOxford/cgat/obsolete/pipeline_kamilah.py/buildFilteredAlignment