circos pipeline

# /usr/bin/env python# coding=utf-8####################################  Author : yunkeli#  Version : 1.0(2015/6/20)#  E-mail : [email protected]###################################import osimport argparseimport reimport randomdef vcf_SNPdensity(snpvcffile,pathway):   print "this step is vcf to SNPdensity "   cmdvcftorate = "/home/liyunke/vcftools_0.1.12b/bin/vcftools --vcf "+snpvcffile+" --out " + pathway+"/SNPdensity100K --SNPdensity 1000000"   result_analysis=os.popen(cmdvcftorate)   print result_analysis.read()def density(SNPdensityfile,pathway):   print "##############################"   print "this step is vcf to densitysplit cat "   fileopen = open(SNPdensityfile).readlines()[1:]   savename = pathway+"/"+"SNPdensity50K.snpden.new.txt"   filesave = open(savename,"w+")   for i in fileopen:      listi = i.split()      filesave.write(listi[0].replace("chr","hs")+"\t"+listi[1]+"\t"+str(int(listi[1])+999999)+"\t"+str(float(listi[3])/10)+"\n")   filesave.close()def densitysplit(SNPdensityfile,pathway):   print "##############################"   print "this step is vcf to densitysplit "   fileopen = open(SNPdensityfile).readlines()[1:]   namelist = []   for i in fileopen:      if i.split()[0] not in namelist:         namelist.append(i.split()[0])   for j in namelist:      savename = pathway+"/"+j.replace("chr","hs")+".snp.txt"      filesave = open(savename,"w+")      for x in fileopen:         listx = x.split()         if listx[0] == j:            filesave.write(listx[0].replace("chr","hs")+"\t"+listx[1]+"\t"+str(int(listx[1])+499999)+"\t"+listx[3]+"\n")      filesave.close()   print "densitysplit ok"def sv_split(svdensityfile,pathway):   print "##############################"   print "this step is vcf to sv_file split "   fileopen = open(svdensityfile).readlines()[1:]   namelist = []   for i in fileopen:      if i.split()[0] not in namelist:         namelist.append(i.split()[0])   for j in namelist:      listrandom = []      savename = pathway+"/"+j.replace("chr","hs")+".sv.txt"      filesave = open(savename,"w+")      for x in fileopen:         listx = x.split()         if listx[0] == j:            if listx[0] != listx[5]:               listrandom.append(x)      if len(listrandom) > 10:         slicelist = random.sample(listrandom, 10)         for links in slicelist:            listlinks = links.split()            filesave.write("segdups"+str(listrandom.index(links))+"\t"+"\t".join(listlinks[0:3]).replace("chr","hs")+"\n")            filesave.write("segdups"+str(listrandom.index(links))+"\t"+"\t".join(listlinks[5:8]).replace("chr","hs")+"\n")         filesave.close()      else:         for links in listrandom:            listlinks = links.split()            filesave.write("segdups"+str(listrandom.index(links))+"\t"+"\t".join(listlinks[0:3])+"\n")            filesave.write("segdups"+str(listrandom.index(links))+"\t"+"\t".join(listlinks[5:8])+"\n")         filesave.close()def circos_config(npath,prefix):   oldconfig = "/home/liyunke/circos/sof/circos-0.67-7/work/pipeline/etc/config"   configopen = open(oldconfig).read()   f1 = re.sub("pathway",npath,configopen)   newconfig = "/home/liyunke/circos/sof/circos-0.67-7/work/pipeline/etc/"+prefix+".conf"   newconfigsave = open(newconfig,"w+")   newconfigsave.write(f1)   newconfigsave.close()def main():   p = argparse.ArgumentParser(usage=‘./circos.pipline.py [--vcf] [--sv] [--prefix] [--outdir] ‘, description=‘circos snp sv‘)     p.add_argument(‘-v‘,‘--vcf‘, type=str, help=‘vcf file‘)     p.add_argument(‘-s‘,‘--sv‘,  type=str, help=‘sv file‘)   p.add_argument(‘-p‘,‘--prefix‘, default="circostest",help=‘prefix or usrname‘)   p.add_argument(‘-o‘,‘--outdir‘, default="./", help=‘document directory‘)   args = p.parse_args()   prefix = args.prefix   vcffile = args.vcf   outdir = args.outdir   vcf_SNPdensity(vcffile,outdir)   SNPdensityfile = outdir+"/SNPdensity100K.snpden"   density(SNPdensityfile,outdir)   densitysplit(SNPdensityfile,outdir)   svdensityfile = args.sv   sv_split(svdensityfile,outdir)   circos_config(outdir,prefix)   cmdstr = "/home/liyunke/circos/sof/circos-0.67-7/bin/circos  -conf /home/liyunke/circos/sof/circos-0.67-7/work/pipeline/etc/"+prefix+".conf --outputdir "+ outdir+" -outputfile "+prefix   result_analysis_circos =os.popen(cmdstr)   print result_analysis_circos.read()   rmcmd = "rm "+ outdir +"/hs*"   result_analysis_rm =os.popen(rmcmd)   print result_analysis_rm.read()if __name__ == ‘__main__‘:   main()