# /usr/bin/env python # coding=utf-8 ################################### #  Author : yunkeli #  Version : 1.0(2015/6/20) #  E-mail : 1316014512@qq.com ################################### import os import argparse import re import random def 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()