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11
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1
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2 import random,string,os,sys
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3
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4
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5 def getScore(intvfile,outfile,summary_type,bwfilepath,nbin,strand,outplot,span):
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6 f = open(intvfile)
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7 tmpsh = "".join(random.sample(string.letters+string.digits, 8))
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8 tmpout = "".join(random.sample(string.letters+string.digits, 8))
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9 tmp = open(tmpsh,'w')
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10 if os.path.isdir(bwfilepath):
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11 for line in f:
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12 flds = line.strip().split('\t')
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13 cmd = 'bigWigSummary -type='+summary_type+' '+bwfilepath+'/'+flds[0]+'.bw '+flds[0]+' '+flds[1]+' '+flds[2]+' '+nbin+' >> '+tmpout+' 2>>'+tmpout+'\n'
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14 tmp.write(cmd)
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15 else:
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16 for line in f:
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17 flds = line.strip().split('\t')
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18 cmd = 'bigWigSummary -type='+summary_type+' '+bwfilepath+' '+flds[0]+' '+flds[1]+' '+flds[2]+' '+nbin+' >> '+tmpout+' 2>>'+tmpout+'\n'
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19 tmp.write(cmd)
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20 f.close()
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21 # remove blank lines
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22 tmp.write("sed '/^$/d' "+tmpout+'>'+tmpout+".1\n")
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23 tmp.write("sed '/^Can/d' "+tmpout+".1 >"+tmpout+".2\n")
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24 # set n/a to 0
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25 tmp.write("sed 's/n\/a/0/g' "+tmpout+".2 >"+tmpout+".3\n")
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26 # replace text with 0
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27 zeros = ''.join(['0\t']*int(nbin))
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28 tmp.write("sed 's/^[a-zA-Z]/"+zeros+"/' "+tmpout+".3 >"+tmpout+".4\n")
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29 # cut the first nbin columns
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30 tmp.write("cut -f 1-"+nbin+" "+tmpout+".4 > "+tmpout+".5\n")
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31 tmp.write("paste "+intvfile+" "+tmpout+".5 >"+outfile+"\n")
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32 tmp.close()
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33 os.system('chmod +x '+tmpsh)
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34 os.system('./'+tmpsh)
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35 #os.system('rm '+tmpout+'*')
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36 #os.system('rm '+tmpsh)
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37
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38 # strandness: need to reverse bins for - strand
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39 if nbin > 1 and strand > 0:
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40 strand = strand - 1 # python is 0 based
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41 os.system('mv '+outfile+' '+tmpout)
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42 f = open(tmpout)
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43 out = open(outfile,'w')
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44 for line in f:
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45 flds=line.strip().split('\t')
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46 if flds[strand] == '+':
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47 out.write(line)
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48 else:
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49 scores = flds[-int(nbin):]
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50 scores.reverse()
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51 flds = flds[:-int(nbin)]+scores
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52 out.write('\t'.join(flds)+'\n')
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53 os.system('rm '+tmpout)
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54 f.close()
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55 out.close()
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56 # plot
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57 if int(nbin) > 1:
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58 rscript = open(tmpsh,"w")
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59 rscript.write("options(warn=-1)\n")
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60 rscript.write("x <- read.table('"+outfile+"',sep='\t')\n")
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61 rscript.write("x <- x[,(ncol(x)+1-"+nbin+"):ncol(x)]\n")
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62 rscript.write("pdf('"+outplot+"')\n")
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63 rscript.write("avg <- apply(x,2,mean)\n")
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64 rscript.write("err <- apply(x,2,sd)/sqrt(nrow(x))\n")
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65 rscript.write("ylim=c(min(avg-err),max(avg+err))\n")
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66 rscript.write("xticks <- seq(ncol(x))-(1+ncol(x))/2\n")
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67 if span >= 0.1:
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68 rscript.write("avg = loess(avg~xticks,span="+str(span)+")$fitted\n")
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69 rscript.write("err = loess(err~xticks,span="+str(span)+")$fitted\n")
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70 rscript.write("par(cex=1.5)\n")
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71 rscript.write("plot(xticks,avg,ylab='average conservation score',xlab='relative position (bin)',type='l',lwd=0,ylim=ylim)\n")
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72 rscript.write("polygon(c(xticks,rev(xticks)),c(avg+err,rev(avg-err)),col='slateblue1',border=NA)\n")
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73 rscript.write("lines(xticks,avg,type='l',lwd=1)\n")
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74 rscript.write("dev.off()\n")
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75 rscript.close()
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76 os.system("R --vanilla < "+tmpsh)
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77 os.system("rm "+tmpsh)
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78
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79 getScore(sys.argv[1],sys.argv[2],sys.argv[3],sys.argv[4],sys.argv[5],int(sys.argv[6]),sys.argv[7],float(sys.argv[8]))
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