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11
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1 '''
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2 align mulitple bed to one bed
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3 python align_multiple.py hmChIP_mm9_peak_bed/mm9-GSE19999_PolII_P25_all.cod.bed hmChIP_mm9_peak_bed/ test.txt test.pdf 100 5000
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4 '''
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5
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6 import os,sys,random
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7 def main():
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8 queryfile = sys.argv[1]
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9 inpath = sys.argv[2]
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10 outputdata = sys.argv[3]
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11 outputerr = sys.argv[4]
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12 barplotpdf = sys.argv[5]
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13 min_feat = sys.argv[6] # min features overlap
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14 windowsize = sys.argv[7]
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15 anchor = sys.argv[8]
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16 span = sys.argv[9] # loess smooth parameter
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17
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18 inpath = inpath.rstrip('/')
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19 #os.system('rm '+inpath+'/*tmp*')
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20
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21 infiles = os.listdir(inpath)
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22
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23 #print len(infiles),' files\n'
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24 i = 0
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25 for infile in infiles:
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26 if 'tmp' in infile:
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27 #os.system('rm '+inpath+'/'+infile)
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28 continue
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29 i = i +1
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30 print i,infile
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31 output = infile.split('/')[-1]+'-to-'+queryfile.split('/')[-1]#'.summary'
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32 if anchor == 'database':
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33 command = 'python /Users/xuebing/galaxy-dist/tools/mytools/alignr.py -b '+inpath+'/'+infile+' -a '+queryfile+' -o '+output+' --summary-only -q -w '+windowsize
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34 else:
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35 command = 'python /Users/xuebing/galaxy-dist/tools/mytools/alignr.py -a '+inpath+'/'+infile+' -b '+queryfile+' -o '+output+' --summary-only -q -w '+windowsize
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36 #print command+'\n'
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37 os.system(command)
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38 print 'start visualization...'
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39 # visualize
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40 rscriptfile = 'f-'+str(random.random())+'.r'
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41 r = open(rscriptfile,'w')
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42 r.write("files <- dir('.','summary',full.name=T)\n")
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43 #r.write("print(files)\n")
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44 r.write("x <- read.table(files[1])\n")
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45 r.write("err <- read.table(gsub('summary','standarderror',files[1]))\n")
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46 r.write("for (filename in files[2:length(files)]){\n")
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47 r.write(" x <- rbind(x,read.table(filename))\n")
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48 r.write(" err <- rbind(err,read.table(gsub('summary','standarderror',filename)))\n")
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49 r.write("}\n")
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50 r.write("x <- x[x[,2] > "+min_feat+",]\n")
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51 r.write("err <- err[err[,2] > "+min_feat+",]\n")
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52 r.write("name <- as.character(x[,1])\n")
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53 r.write("nfeat <- x[,2]\n")
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54 r.write("x <- x[,3:ncol(x)]\n")
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55 r.write("err <- err[,3:ncol(err)]\n")
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56 r.write("for (i in 1:nrow(x)) {\n")
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57 r.write(" name[i] <- strsplit(name[i],'-to-')[[1]][1]\n")
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58 r.write("}\n")
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59 # remove rows that have no variation, which cause problem in heatmap. This is the case when align to itself
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60 r.write("toremove <- seq(nrow(x))\n")
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61 r.write("for (i in 1:nrow(x)){\n")
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62 r.write(" toremove[i] <- all(x[i,] == x[i,1])\n")
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63 r.write("}\n")
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64 r.write("x <- x[!toremove,]\n")
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65 r.write("err <- err[!toremove,]\n")
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66 r.write("name <- name[!toremove]\n")
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67 r.write("nfeat <- nfeat[!toremove]\n")
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68 r.write("write.table(cbind(name,nfeat,x),file='"+outputdata+"',sep ='\\t',quote=F,row.names=F,col.names=F)\n")
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69 r.write("write.table(cbind(name,nfeat,err),file='"+outputerr+"',sep ='\\t',quote=F,row.names=F,col.names=F)\n")
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70
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71 r.write("pdf('"+barplotpdf+"')\n")
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72 r.write("heatmap(t(scale(t(as.matrix(x,nc=ncol(x))))),Colv=NA,labRow=name,labCol=NA,margins=c(1,8),cexRow=0.02+1/log(nrow(x)),col=heat.colors(1000))\n")
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73
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74 if windowsize != '0' :
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75 r.write("xticks <- seq(-"+windowsize+","+windowsize+",length.out=100)\n")
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76 r.write("xlab <- 'relative position (bp)'\n")
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77 else:
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78 r.write("xticks <- seq(100)\n")
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79 r.write("xlab <- 'relative position (bin)'\n")
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80
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81 #r.write("plot(xticks,colSums(t(scale(t(as.matrix(x,nc=ncol(x)))))),xlab='relative position (bp)',type='l',lwd=2,main='total signal')\n")
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82 r.write("for (i in 1:nrow(x)) {\n")
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83 r.write(" avg <- x[i,]/nfeat[i]\n")
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84 #r.write(" maxv <- max(avg)\n")
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85 #r.write(" minv <- min(avg)\n")
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86 #r.write(" medv <- median(avg)\n")
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87 #r.write(" if (maxv < "+fold+"*medv | minv*"+fold+">medv){next}\n")
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88 #smooth
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89 if float(span) >= 0.1:
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90 r.write(" avg = loess(as.numeric(avg)~xticks,span="+span+")$fitted\n")
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91 r.write(" err[i,] = loess(as.numeric(err[i,])~xticks,span="+span+")$fitted\n")
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92 r.write(" par(cex=1.5)\n")
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93 r.write(" plot(xticks,avg,ylab='average coverage',main=paste(name[i],'\n n=',nfeat[i],sep=''),xlab=xlab,type='l',lwd=1,ylim=c(min(avg-err[i,]),max(avg+err[i,])))\n")
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94 r.write(" polygon(c(xticks,rev(xticks)),c(avg+err[i,],rev(avg-err[i,])),col='slateblue1',border=NA)\n")
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95 r.write(" lines(xticks,avg,type='l',lwd=1)\n")
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96 r.write("}\n")
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97 r.write("dev.off()\n")
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98 r.close()
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99 os.system("R --vanilla < "+rscriptfile)
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100 os.system('rm '+rscriptfile)
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101 os.system('rm *.summary')
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102 os.system('rm *.standarderror')
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103
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104 main()
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