def HiCSpector_wrapper(outdir,parameters,concise_analysis,samplename1,samplename2,chromo,running_mode,f1,f2,nodefile):
script_comparison_file=outdir+'/scripts/HiC-spector/'+samplename1+'.'+samplename2+'/'+chromo+'.'+samplename1+'.'+samplename2+'.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')
if os.path.isfile(f1) and os.path.getsize(f1)>20:
if os.path.isfile(f2) and os.path.getsize(f2)>20:
outpath=outdir+'/results/reproducibility/'+samplename1+'.vs.'+samplename2+'/HiC-Spector/'+chromo+'.'+samplename1+'.vs.'+samplename2+'.scores.txt'
subp.check_output(['bash','-c','mkdir -p '+os.path.dirname(outpath)])
script_comparison.write("$mypython -W ignore "+os.path.abspath(os.path.dirname(os.path.dirname(os.path.realpath(__file__))))+"/reproducibility_analysis/hic-spector_wrapper.py --m1 "+f1+" --m2 "+f2+" --out "+outpath+".printout --node_file "+nodefile+" --num_evec "+parameters['HiC-Spector']['n']+"\n")
script_comparison.write("cat "+outpath+".printout | tail -n1 | cut -f2 | awk '{print \""+samplename1+"\\t"+samplename2+"\\t\"$3}' > "+outpath+'\n')
script_comparison.write("rm "+outpath+".printout"+'\n')
script_comparison.close()
run_script(script_comparison_file,running_mode)
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