def QuASAR_rep_wrapper(outdir,parameters,samplename1,samplename2,running_mode):
script_comparison_file=outdir+'/scripts/QuASAR-Rep/'+samplename1+'.vs.'+samplename2+'/'+samplename1+'.vs.'+samplename2+'.QuASAR-Rep.sh'
subp.check_output(['bash','-c','mkdir -p '+os.path.dirname(script_comparison_file)])
script_comparison=open(script_comparison_file,'w')
script_comparison.write("#!/bin/sh"+'\n')
script_comparison.write('. '+bashrc_file+'\n')
outpath=outdir+'/results/reproducibility/'+samplename1+'.vs.'+samplename2+'/QuASAR-Rep/'+samplename1+'.vs.'+samplename2+'.QuASAR-Rep.scores.txt'
subp.check_output(['bash','-c','mkdir -p '+os.path.dirname(outpath)])
quasar_data=outdir+'/data/forQuASAR'
quasar_transform1=quasar_data+'/'+samplename1+'.quasar_transform'
quasar_transform2=quasar_data+'/'+samplename2+'.quasar_transform'
script_comparison.write('${mypython} '+os.path.dirname(os.path.dirname(os.path.abspath(os.path.dirname(os.path.realpath(__file__)))))+"/hifive/bin/find_quasar_replicate_score"+' '+quasar_transform1+' '+quasar_transform2+' '+outpath+'\n')
script_comparison.write('${mypython} '+os.path.abspath(os.path.dirname(os.path.realpath(__file__)))+"/plot_quasar_scatter.py"+' '+quasar_transform1+' '+quasar_transform2+' '+outpath+'\n')
#split the scores by chromosomes
script_comparison.write('${mypython} '+os.path.abspath(os.path.dirname(os.path.realpath(__file__)))+"/quasar_split_by_chromosomes.py"+' '+outpath+'\n')
script_comparison.close()
run_script(script_comparison_file,running_mode)
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