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