@follows( buildGeneMatrixConsequences,
          buildGeneMatrixAlleles,
          buildGeneMatrixEffects,
          buildGeneMatrixStructuralVariants)
@files( [ ((x,y), "%s_vs_%s.gla" % (re.sub(".genematrix", "", x), \
                                    re.sub("assignments.", "", y) ) )\
              for x,y in \
              itertools.product( \
            glob.glob("*.genematrix" ),
            glob.glob("assignments.*") ) 
          if not y.endswith(".log") ] )
def runGeneListAnalysis( infiles, outfile):
    '''run a gene list analysis.'''

    genematrix, assignments = infiles

    to_cluster = True

    try:
        options = "--qvalue-lambda=%(genelist_analysis_qvalue_lambda)f" % PARAMS
    except __HOLE__:
        options = ""

    statement = '''
    python %(scriptsdir)s/genelist_analysis.py 
           --format=matrix 
           --filename-assignments=%(assignments)s 
           --fdr 
           --qvalue-method=%(genelist_analysis_qvalue_method)s
           --log=%(outfile)s.log
           %(options)s
    < %(genematrix)s
    > %(outfile)s
    '''
    
    P.run()

###########################################################################
dataset/ETHPy150Open CGATOxford/cgat/obsolete/pipeline_snps.py/runGeneListAnalysis