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76
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1 library(reshape2)
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2
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3 args <- commandArgs(trailingOnly = TRUE)
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4
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5 gene.matches = args[1]
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6 sequence.file = args[2]
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7 outputdir = args[3]
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8 main.html = "index.html"
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9
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10 setwd(outputdir)
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11
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12 genes = read.table(gene.matches, header=T, sep="\t", fill=T)
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13 sequences = read.table(sequence.file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
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14
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15 dat = merge(sequences, genes, by="Sequence.ID")
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16
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17 dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT, dat$FR2.IMGT, dat$FR3.IMGT)
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18
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19 IDs = dat[,c("Sequence.ID", "seq_conc", "best_match")]
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20 IDs$best_match = as.character(IDs$best_match)
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21
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22 #dat = data.frame(data.table(dat)[, list(freq=.N), by=c("best_match", "seq_conc")])
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23
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24 dat = data.frame(table(dat$best_match, dat$seq_conc))
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25
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26 dat = dat[dat$Freq > 1,]
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27
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28 names(dat) = c("best_match", "seq_conc", "Freq")
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29
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30 dat$seq_conc = factor(dat$seq_conc)
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31
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32 dat = dat[order(nchar(as.character(dat$seq_conc))),]
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33
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34 #writing html from R...
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35 td = function(val) { paste("<td>", val, "</td>", sep="") }
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36 tr = function(val) { capture.output(cat("<tr>", td(val), "</tr>", sep="")) }
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37 make.link = function(id, clss, val) { paste("<a href='", clss, "_", id, ".html'>", val, "</a>", sep="") }
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38 tbl = function(df) { res = "<table border='1'>"; for(i in 1:nrow(df)){ res = paste(res, tr(df[i,]), sep=""); }; res = paste(res, "</table>"); }
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39
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40 cat("<table border='1'>", file=main.html, append=F)
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41 cat("<tr><th>Sequence</th><th>ca1</th><th>ca2</th><th>cg1</th><th>cg2</th><th>cg3</th><th>cg4</th><th>cm</th></tr>", file=main.html, append=T)
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42
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43 for(i in 1:nrow(dat)){
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44 ca1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca1",]
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45 ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca2",]
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46
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47 cg1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg1",]
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48 cg2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg2",]
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49 cg3 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg3",]
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50 cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg4",]
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51
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52 cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cm",]
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53
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54 id = as.numeric(dat[i,"seq_conc"])
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55
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56 if(nrow(ca1) > 0){
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57 cat(tbl(ca1), file=paste("ca1_", id, ".html", sep=""))
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58 }
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59
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60 if(nrow(ca2) > 0){
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61 cat(tbl(ca2), file=paste("ca2_", id, ".html", sep=""))
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62 }
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63
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64 if(nrow(cg1) > 0){
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65 cat(tbl(cg1), file=paste("cg1_", id, ".html", sep=""))
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66 }
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67
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68 if(nrow(cg2) > 0){
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69 cat(tbl(cg2), file=paste("cg2_", id, ".html", sep=""))
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70 }
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71
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72 if(nrow(cg3) > 0){
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73 cat(tbl(cg3), file=paste("cg3_", id, ".html", sep=""))
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74 }
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75
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76 if(nrow(cg4) > 0){
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77 cat(tbl(cg4), file=paste("cg4_", id, ".html", sep=""))
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78 }
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79
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80 if(nrow(cm) > 0){
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81 cat(tbl(cm), file=paste("cm_", id, ".html", sep=""))
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82 }
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83
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84 ca1.html = make.link(id, "ca1", nrow(ca1))
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85 ca2.html = make.link(id, "ca2", nrow(ca2))
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86
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87 cg1.html = make.link(id, "cg1", nrow(cg1))
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88 cg2.html = make.link(id, "cg2", nrow(cg2))
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89 cg3.html = make.link(id, "cg3", nrow(cg3))
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90 cg4.html = make.link(id, "cg4", nrow(cg4))
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91
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92 cm.html = make.link(id, "cm", nrow(cm))
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93
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94 rw = c(as.character(dat[i,"seq_conc"]), ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html)
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95
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96 cat(tr(rw), file=main.html, append=T)
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97 }
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98
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99 cat("</table>", file=main.html, append=T)
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