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1 import sys,os
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2
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3 infile = sys.argv[1]
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4 outfile = sys.argv[2]
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5 uselog = sys.argv[3]
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6 subset = sys.argv[4]
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7 reorder = sys.argv[5]
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8 color = sys.argv[6]
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9 scale = sys.argv[7] # rescale each row
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10 rscript = open('tmp.r','w')
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11
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12 rscript.write("x <- read.table('"+infile+"')\n")
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13 rscript.write("nfeat <- nrow(x) \n")
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14 rscript.write("nbin <- ncol(x) - 2\n")
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15 rscript.write("totalcov <- x[,2]\n")
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16 rscript.write("x <- x[,3:ncol(x)]\n")
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17
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18 if subset =='subset':
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19 rscript.write("if (nfeat*nbin > 100000) {\n")
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20 rscript.write(" nfeat2 <- as.integer(100000/nbin)\n")
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21 rscript.write(" subind <- sample(seq(nfeat),nfeat2)\n")
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22 rscript.write(" x <- x[subind,]\n")
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23 rscript.write(" totalcov <- totalcov[subind]\n")
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24 rscript.write("}\n")
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25
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26 rscript.write("pdf('"+outfile+"')\n")
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27
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28 if uselog == 'uselog':
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29 rscript.write("x <- -(log(1+as.matrix(x,nc=ncol(x)-2)))\n")
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30 else:
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31 rscript.write("x <- -as.matrix(x,nc=ncol(x)-2)\n")
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32 if scale == 'scale':
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33 rscript.write("x <- scale(x)\n")
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34 if reorder == 'average':
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35 rscript.write("hc <- hclust(dist(x),method= 'average')\n")
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36 rscript.write("x <- x[hc$order,]\n")
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37 elif reorder == 'centroid':
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38 rscript.write("hc <- hclust(dist(x),method= 'centroid')\n")
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39 rscript.write("x <- x[hc$order,]\n")
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40 elif reorder == 'complete':
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41 rscript.write("hc <- hclust(dist(x),method= 'complete')\n")
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42 rscript.write("x <- x[hc$order,]\n")
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43 elif reorder == 'single':
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44 rscript.write("hc <- hclust(dist(x),method= 'single')\n")
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45 rscript.write("x <- x[hc$order,]\n")
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46 elif reorder == 'median':
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47 rscript.write("hc <- hclust(dist(x),method= 'median')\n")
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48 rscript.write("x <- x[hc$order,]\n")
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49 elif reorder == 'sort_by_total':
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50 rscript.write("srt <- sort(totalcov,index.return=T)\n")
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51 rscript.write("x <- x[srt$ix,]\n")
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52 elif reorder == 'sort_by_center':
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53 rscript.write("srt <- sort(x[,as.integer(nbin/2)],index.return=T)\n")
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54 rscript.write("x <- x[srt$ix,]\n")
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55 if color == 'heat':
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56 rscript.write("colormap = heat.colors(1000)\n")
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57 elif color == 'topo':
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58 rscript.write("colormap = topo.colors(1000)\n")
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59 elif color == 'rainbow':
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60 rscript.write("colormap = rainbow(1000)\n")
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61 elif color == 'terrain':
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62 rscript.write("colormap = terrain.colors(1000)\n")
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63 else:
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64 rscript.write("colormap = gray.colors(1000)\n")
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65
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66 #rscript.write("qt <- quantile(as.vector(x),probs=c(0.1,0.9))\n")
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67 #rscript.write("breaks <- c(min(as.vector(x)),seq(qt[1],qt[2],length.out=99),max(as.vector(x)))\n")
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68 #rscript.write("image(t(x),col=colormap,breaks=breaks,axes=F)\n")
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69 rscript.write("image(t(x),col=colormap,axes=F)\n")
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70 rscript.write("dev.off()\n")
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71
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72 rscript.close()
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73
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74 os.system("R --slave < tmp.r")
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75 os.system("rm tmp.r")
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76
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