annotate sequence_overview.r @ 81:b6f9a640e098 draft

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author davidvanzessen
date Fri, 19 Feb 2021 15:10:54 +0000
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81
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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 before.unique.file = args[1]
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6 merged.file = args[2]
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7 outputdir = args[3]
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8 gene.classes = unlist(strsplit(args[4], ","))
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9 hotspot.analysis.sum.file = args[5]
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10 NToverview.file = paste(outputdir, "ntoverview.txt", sep="/")
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11 NTsum.file = paste(outputdir, "ntsum.txt", sep="/")
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12 main.html = "index.html"
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13 empty.region.filter = args[6]
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14
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15
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16 setwd(outputdir)
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17
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18 before.unique = read.table(before.unique.file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
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19 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
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20 hotspot.analysis.sum = read.table(hotspot.analysis.sum.file, header=F, sep=",", fill=T, stringsAsFactors=F, quote="")
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21
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22 #before.unique = before.unique[!grepl("unmatched", before.unique$best_match),]
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23
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24 if(empty.region.filter == "leader"){
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25 before.unique$seq_conc = paste(before.unique$FR1.IMGT.seq, before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)
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26 } else if(empty.region.filter == "FR1"){
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27 before.unique$seq_conc = paste(before.unique$CDR1.IMGT.seq, before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)
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28 } else if(empty.region.filter == "CDR1"){
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29 before.unique$seq_conc = paste(before.unique$FR2.IMGT.seq, before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)
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30 } else if(empty.region.filter == "FR2"){
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31 before.unique$seq_conc = paste(before.unique$CDR2.IMGT.seq, before.unique$FR3.IMGT.seq, before.unique$CDR3.IMGT.seq)
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32 }
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33
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34 IDs = before.unique[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")]
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35 IDs$best_match = as.character(IDs$best_match)
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36
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37 dat = data.frame(table(before.unique$seq_conc))
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38
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39 names(dat) = c("seq_conc", "Freq")
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40
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41 dat$seq_conc = factor(dat$seq_conc)
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42
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43 dat = dat[order(as.character(dat$seq_conc)),]
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44
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45 #writing html from R...
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46 get.bg.color = function(val){
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47 if(val %in% c("TRUE", "FALSE", "T", "F")){ #if its a logical value, give the background a green/red color
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48 return(ifelse(val,"#eafaf1","#f9ebea"))
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49 } else if (!is.na(as.numeric(val))) { #if its a numerical value, give it a grey tint if its >0
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50 return(ifelse(val > 0,"#eaecee","white"))
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51 } else {
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52 return("white")
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53 }
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54 }
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55 td = function(val) {
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56 return(paste("<td bgcolor='", get.bg.color(val), "'>", val, "</td>", sep=""))
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57 }
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58 tr = function(val) {
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59 return(paste(c("<tr>", sapply(val, td), "</tr>"), collapse=""))
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60 }
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61
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62 make.link = function(id, clss, val) {
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63 paste("<a href='", clss, "_", id, ".html'>", val, "</a>", sep="")
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64 }
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65 tbl = function(df) {
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66 res = "<table border='1'>"
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67 for(i in 1:nrow(df)){
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68 res = paste(res, tr(df[i,]), sep="")
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69 }
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70 res = paste(res, "</table>")
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71 }
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72
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73 cat("<center><img src='data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAA8AAAAPCAYAAAA71pVKAAAAzElEQVQoka2TwQ2CQBBFpwTshw4ImW8ogJMlUIMmhNCDxgasAi50oSXA8XlAjCG7aqKTzGX/vsnM31mzR0gk7tTudO5MEizpzvQ4ryUSe408J3Xn+grE0p1rnpOamVmWsZG4rS+dzzAMsN8Hi9yyjI1JNGtxu4VxBJgLRLpoTKIPiW0LlwtUVRTubW2OBGUJu92cZRmdfbKQMAw8o+vi5v0fLorZ7Y9waGYJjsf38DJz0O1PsEQffOcv4Sa6YYfDDJ5Obzbsp93+5VfdATueO1fdLdI0AAAAAElFTkSuQmCC'> Please note that this tab is based on all sequences before filter unique sequences and the remove duplicates based on filters are applied. In this table only sequences occuring more than once are included. </center>", file=main.html, append=F)
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74 cat("<table border='1' class='pure-table pure-table-striped'>", file=main.html, append=T)
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75
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76 if(empty.region.filter == "leader"){
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77 cat("<caption>FR1+CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
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78 } else if(empty.region.filter == "FR1"){
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79 cat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
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80 } else if(empty.region.filter == "CDR1"){
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81 cat("<caption>FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
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82 } else if(empty.region.filter == "FR2"){
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83 cat("<caption>CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
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84 }
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85
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86 cat("<tr>", file=main.html, append=T)
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87 cat("<th>Sequence</th><th>Functionality</th><th>IGA1</th><th>IGA2</th><th>IGG1</th><th>IGG2</th><th>IGG3</th><th>IGG4</th><th>IGM</th><th>IGE</th><th>UN</th>", file=main.html, append=T)
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88 cat("<th>total IGA</th><th>total IGG</th><th>total IGM</th><th>total IGE</th><th>number of subclasses</th><th>present in both IGA and IGG</th><th>present in IGA, IGG and IGM</th><th>present in IGA, IGG and IGE</th><th>present in IGA, IGG, IGM and IGE</th><th>IGA1+IGA2</th>", file=main.html, append=T)
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89 cat("<th>IGG1+IGG2</th><th>IGG1+IGG3</th><th>IGG1+IGG4</th><th>IGG2+IGG3</th><th>IGG2+IGG4</th><th>IGG3+IGG4</th>", file=main.html, append=T)
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90 cat("<th>IGG1+IGG2+IGG3</th><th>IGG2+IGG3+IGG4</th><th>IGG1+IGG2+IGG4</th><th>IGG1+IGG3+IGG4</th><th>IGG1+IGG2+IGG3+IGG4</th>", file=main.html, append=T)
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91 cat("</tr>", file=main.html, append=T)
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92
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93
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94
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95 single.sequences=0 #sequence only found once, skipped
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96 in.multiple=0 #same sequence across multiple subclasses
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97 multiple.in.one=0 #same sequence multiple times in one subclass
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98 unmatched=0 #all of the sequences are unmatched
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99 some.unmatched=0 #one or more sequences in a clone are unmatched
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100 matched=0 #should be the same als matched sequences
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101
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102 sequence.id.page="by_id.html"
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103
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104 for(i in 1:nrow(dat)){
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105
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106 ca1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGA1", IDs$best_match),]
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107 ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGA2", IDs$best_match),]
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108
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109 cg1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG1", IDs$best_match),]
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110 cg2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG2", IDs$best_match),]
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111 cg3 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG3", IDs$best_match),]
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112 cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG4", IDs$best_match),]
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113
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114 cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGM", IDs$best_match),]
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115
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116 ce = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGE", IDs$best_match),]
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117
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118 un = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^unmatched", IDs$best_match),]
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119
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120 allc = rbind(ca1, ca2, cg1, cg2, cg3, cg4, cm, ce, un)
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121
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122 ca1.n = nrow(ca1)
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123 ca2.n = nrow(ca2)
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124
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125 cg1.n = nrow(cg1)
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126 cg2.n = nrow(cg2)
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127 cg3.n = nrow(cg3)
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128 cg4.n = nrow(cg4)
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129
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130 cm.n = nrow(cm)
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131
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132 ce.n = nrow(ce)
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133
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134 un.n = nrow(un)
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135
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136 classes = c(ca1.n, ca2.n, cg1.n, cg2.n, cg3.n, cg4.n, cm.n, ce.n, un.n)
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137
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138 classes.sum = sum(classes)
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139
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140 if(classes.sum == 1){
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141 single.sequences = single.sequences + 1
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142 next
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143 }
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144
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145 if(un.n == classes.sum){
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146 unmatched = unmatched + 1
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147 next
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148 }
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149
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150 classes.no.un = classes[-length(classes)]
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151
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152 in.classes = sum(classes.no.un > 0)
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153
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154 matched = matched + in.classes #count in how many subclasses the sequence occurs.
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155
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156 if(any(classes == classes.sum)){
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157 multiple.in.one = multiple.in.one + 1
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158 } else if (un.n > 0) {
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159 some.unmatched = some.unmatched + 1
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160 } else {
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161 in.multiple = in.multiple + 1
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162 }
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163
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164 id = as.numeric(dat[i,"seq_conc"])
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165
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166 functionality = paste(unique(allc[,"Functionality"]), collapse=",")
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167
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davidvanzessen
parents:
diff changeset
168 by.id.row = c()
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davidvanzessen
parents:
diff changeset
169
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davidvanzessen
parents:
diff changeset
170 if(ca1.n > 0){
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davidvanzessen
parents:
diff changeset
171 cat(tbl(ca1), file=paste("IGA1_", id, ".html", sep=""))
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davidvanzessen
parents:
diff changeset
172 }
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davidvanzessen
parents:
diff changeset
173
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davidvanzessen
parents:
diff changeset
174 if(ca2.n > 0){
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davidvanzessen
parents:
diff changeset
175 cat(tbl(ca2), file=paste("IGA2_", id, ".html", sep=""))
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davidvanzessen
parents:
diff changeset
176 }
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davidvanzessen
parents:
diff changeset
177
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davidvanzessen
parents:
diff changeset
178 if(cg1.n > 0){
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davidvanzessen
parents:
diff changeset
179 cat(tbl(cg1), file=paste("IGG1_", id, ".html", sep=""))
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davidvanzessen
parents:
diff changeset
180 }
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davidvanzessen
parents:
diff changeset
181
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davidvanzessen
parents:
diff changeset
182 if(cg2.n > 0){
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davidvanzessen
parents:
diff changeset
183 cat(tbl(cg2), file=paste("IGG2_", id, ".html", sep=""))
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davidvanzessen
parents:
diff changeset
184 }
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davidvanzessen
parents:
diff changeset
185
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davidvanzessen
parents:
diff changeset
186 if(cg3.n > 0){
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davidvanzessen
parents:
diff changeset
187 cat(tbl(cg3), file=paste("IGG3_", id, ".html", sep=""))
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davidvanzessen
parents:
diff changeset
188 }
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davidvanzessen
parents:
diff changeset
189
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davidvanzessen
parents:
diff changeset
190 if(cg4.n > 0){
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davidvanzessen
parents:
diff changeset
191 cat(tbl(cg4), file=paste("IGG4_", id, ".html", sep=""))
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davidvanzessen
parents:
diff changeset
192 }
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davidvanzessen
parents:
diff changeset
193
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davidvanzessen
parents:
diff changeset
194 if(cm.n > 0){
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davidvanzessen
parents:
diff changeset
195 cat(tbl(cm), file=paste("IGM_", id, ".html", sep=""))
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davidvanzessen
parents:
diff changeset
196 }
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davidvanzessen
parents:
diff changeset
197
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davidvanzessen
parents:
diff changeset
198 if(ce.n > 0){
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davidvanzessen
parents:
diff changeset
199 cat(tbl(ce), file=paste("IGE_", id, ".html", sep=""))
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davidvanzessen
parents:
diff changeset
200 }
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davidvanzessen
parents:
diff changeset
201
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davidvanzessen
parents:
diff changeset
202 if(un.n > 0){
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davidvanzessen
parents:
diff changeset
203 cat(tbl(un), file=paste("un_", id, ".html", sep=""))
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davidvanzessen
parents:
diff changeset
204 }
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davidvanzessen
parents:
diff changeset
205
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davidvanzessen
parents:
diff changeset
206 ca1.html = make.link(id, "IGA1", ca1.n)
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davidvanzessen
parents:
diff changeset
207 ca2.html = make.link(id, "IGA2", ca2.n)
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davidvanzessen
parents:
diff changeset
208
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davidvanzessen
parents:
diff changeset
209 cg1.html = make.link(id, "IGG1", cg1.n)
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davidvanzessen
parents:
diff changeset
210 cg2.html = make.link(id, "IGG2", cg2.n)
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davidvanzessen
parents:
diff changeset
211 cg3.html = make.link(id, "IGG3", cg3.n)
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davidvanzessen
parents:
diff changeset
212 cg4.html = make.link(id, "IGG4", cg4.n)
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davidvanzessen
parents:
diff changeset
213
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davidvanzessen
parents:
diff changeset
214 cm.html = make.link(id, "IGM", cm.n)
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davidvanzessen
parents:
diff changeset
215
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davidvanzessen
parents:
diff changeset
216 ce.html = make.link(id, "IGE", ce.n)
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davidvanzessen
parents:
diff changeset
217
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davidvanzessen
parents:
diff changeset
218 un.html = make.link(id, "un", un.n)
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davidvanzessen
parents:
diff changeset
219
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davidvanzessen
parents:
diff changeset
220 #extra columns
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davidvanzessen
parents:
diff changeset
221 ca.n = ca1.n + ca2.n
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davidvanzessen
parents:
diff changeset
222
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davidvanzessen
parents:
diff changeset
223 cg.n = cg1.n + cg2.n + cg3.n + cg4.n
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davidvanzessen
parents:
diff changeset
224
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davidvanzessen
parents:
diff changeset
225 #in.classes
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davidvanzessen
parents:
diff changeset
226
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davidvanzessen
parents:
diff changeset
227 in.ca.cg = (ca.n > 0 & cg.n > 0)
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davidvanzessen
parents:
diff changeset
228
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davidvanzessen
parents:
diff changeset
229 in.ca.cg.cm = (ca.n > 0 & cg.n > 0 & cm.n > 0)
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davidvanzessen
parents:
diff changeset
230
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davidvanzessen
parents:
diff changeset
231 in.ca.cg.ce = (ca.n > 0 & cg.n > 0 & ce.n > 0)
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davidvanzessen
parents:
diff changeset
232
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davidvanzessen
parents:
diff changeset
233 in.ca.cg.cm.ce = (ca.n > 0 & cg.n > 0 & cm.n > 0 & ce.n > 0)
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davidvanzessen
parents:
diff changeset
234
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davidvanzessen
parents:
diff changeset
235 in.ca1.ca2 = (ca1.n > 0 & ca2.n > 0)
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davidvanzessen
parents:
diff changeset
236
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davidvanzessen
parents:
diff changeset
237 in.cg1.cg2 = (cg1.n > 0 & cg2.n > 0)
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davidvanzessen
parents:
diff changeset
238 in.cg1.cg3 = (cg1.n > 0 & cg3.n > 0)
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davidvanzessen
parents:
diff changeset
239 in.cg1.cg4 = (cg1.n > 0 & cg4.n > 0)
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davidvanzessen
parents:
diff changeset
240 in.cg2.cg3 = (cg2.n > 0 & cg3.n > 0)
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davidvanzessen
parents:
diff changeset
241 in.cg2.cg4 = (cg2.n > 0 & cg4.n > 0)
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davidvanzessen
parents:
diff changeset
242 in.cg3.cg4 = (cg3.n > 0 & cg4.n > 0)
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davidvanzessen
parents:
diff changeset
243
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davidvanzessen
parents:
diff changeset
244 in.cg1.cg2.cg3 = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0)
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davidvanzessen
parents:
diff changeset
245 in.cg2.cg3.cg4 = (cg2.n > 0 & cg3.n > 0 & cg4.n > 0)
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davidvanzessen
parents:
diff changeset
246 in.cg1.cg2.cg4 = (cg1.n > 0 & cg2.n > 0 & cg4.n > 0)
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davidvanzessen
parents:
diff changeset
247 in.cg1.cg3.cg4 = (cg1.n > 0 & cg3.n > 0 & cg4.n > 0)
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davidvanzessen
parents:
diff changeset
248
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davidvanzessen
parents:
diff changeset
249 in.cg.all = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0 & cg4.n > 0)
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davidvanzessen
parents:
diff changeset
250
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davidvanzessen
parents:
diff changeset
251 #rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html)
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davidvanzessen
parents:
diff changeset
252 rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, ce.html, un.html)
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davidvanzessen
parents:
diff changeset
253 rw = c(rw, ca.n, cg.n, cm.n, ce.n, in.classes, in.ca.cg, in.ca.cg.cm, in.ca.cg.ce, in.ca.cg.cm.ce, in.ca1.ca2, in.cg1.cg2, in.cg1.cg3, in.cg1.cg4, in.cg2.cg3, in.cg2.cg4, in.cg3.cg4, in.cg1.cg2.cg3, in.cg2.cg3.cg4, in.cg1.cg2.cg4, in.cg1.cg3.cg4, in.cg.all)
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davidvanzessen
parents:
diff changeset
254
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davidvanzessen
parents:
diff changeset
255
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
256
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davidvanzessen
parents:
diff changeset
257 cat(tr(rw), file=main.html, append=T)
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davidvanzessen
parents:
diff changeset
258
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
259
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davidvanzessen
parents:
diff changeset
260 for(i in 1:nrow(allc)){ #generate html by id
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davidvanzessen
parents:
diff changeset
261 html = make.link(id, allc[i,"best_match"], allc[i,"Sequence.ID"])
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
262 cat(paste(html, "<br />"), file=sequence.id.page, append=T)
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davidvanzessen
parents:
diff changeset
263 }
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davidvanzessen
parents:
diff changeset
264 }
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
265
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davidvanzessen
parents:
diff changeset
266 cat("</table>", file=main.html, append=T)
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davidvanzessen
parents:
diff changeset
267
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davidvanzessen
parents:
diff changeset
268 print(paste("Single sequences:", single.sequences))
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davidvanzessen
parents:
diff changeset
269 print(paste("Sequences in multiple subclasses:", in.multiple))
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davidvanzessen
parents:
diff changeset
270 print(paste("Multiple sequences in one subclass:", multiple.in.one))
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davidvanzessen
parents:
diff changeset
271 print(paste("Matched with unmatched:", some.unmatched))
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davidvanzessen
parents:
diff changeset
272 print(paste("Count that should match 'matched' sequences:", matched))
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davidvanzessen
parents:
diff changeset
273
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davidvanzessen
parents:
diff changeset
274 #ACGT overview
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davidvanzessen
parents:
diff changeset
275
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davidvanzessen
parents:
diff changeset
276 #NToverview = merged[!grepl("^unmatched", merged$best_match),]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
277 NToverview = merged
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
278
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davidvanzessen
parents:
diff changeset
279 if(empty.region.filter == "leader"){
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
280 NToverview$seq = paste(NToverview$FR1.IMGT.seq, NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
281 } else if(empty.region.filter == "FR1"){
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
282 NToverview$seq = paste(NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
283 } else if(empty.region.filter == "CDR1"){
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
284 NToverview$seq = paste(NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
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davidvanzessen
parents:
diff changeset
285 } else if(empty.region.filter == "FR2"){
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
286 NToverview$seq = paste(NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
287 }
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
288
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
289 NToverview$A = nchar(gsub("[^Aa]", "", NToverview$seq))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
290 NToverview$C = nchar(gsub("[^Cc]", "", NToverview$seq))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
291 NToverview$G = nchar(gsub("[^Gg]", "", NToverview$seq))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
292 NToverview$T = nchar(gsub("[^Tt]", "", NToverview$seq))
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davidvanzessen
parents:
diff changeset
293
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davidvanzessen
parents:
diff changeset
294 #Nsum = data.frame(Sequence.ID="-", best_match="Sum", seq="-", A = sum(NToverview$A), C = sum(NToverview$C), G = sum(NToverview$G), T = sum(NToverview$T))
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davidvanzessen
parents:
diff changeset
295
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davidvanzessen
parents:
diff changeset
296 #NToverview = rbind(NToverview, NTsum)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
297
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
298 NTresult = data.frame(nt=c("A", "C", "T", "G"))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
299
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davidvanzessen
parents:
diff changeset
300 for(clazz in gene.classes){
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
301 print(paste("class:", clazz))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
302 NToverview.sub = NToverview[grepl(paste("^", clazz, sep=""), NToverview$best_match),]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
303 print(paste("nrow:", nrow(NToverview.sub)))
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davidvanzessen
parents:
diff changeset
304 new.col.x = c(sum(NToverview.sub$A), sum(NToverview.sub$C), sum(NToverview.sub$T), sum(NToverview.sub$G))
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davidvanzessen
parents:
diff changeset
305 new.col.y = sum(new.col.x)
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davidvanzessen
parents:
diff changeset
306 new.col.z = round(new.col.x / new.col.y * 100, 2)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
307
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
308 tmp = names(NTresult)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
309 NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
310 names(NTresult) = c(tmp, paste(clazz, c("x", "y", "z"), sep=""))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
311 }
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
312
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
313 NToverview.tmp = NToverview[,c("Sequence.ID", "best_match", "seq", "A", "C", "G", "T")]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
314
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
315 names(NToverview.tmp) = c("Sequence.ID", "best_match", "Sequence of the analysed region", "A", "C", "G", "T")
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davidvanzessen
parents:
diff changeset
316
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davidvanzessen
parents:
diff changeset
317 write.table(NToverview.tmp, NToverview.file, quote=F, sep="\t", row.names=F, col.names=T)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
318
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
319 NToverview = NToverview[!grepl("unmatched", NToverview$best_match),]
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
320
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
321 new.col.x = c(sum(NToverview$A), sum(NToverview$C), sum(NToverview$T), sum(NToverview$G))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
322 new.col.y = sum(new.col.x)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
323 new.col.z = round(new.col.x / new.col.y * 100, 2)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
324
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
325 tmp = names(NTresult)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
326 NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
327 names(NTresult) = c(tmp, paste("all", c("x", "y", "z"), sep=""))
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
328
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
329 names(hotspot.analysis.sum) = names(NTresult)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
330
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
331 hotspot.analysis.sum = rbind(hotspot.analysis.sum, NTresult)
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
332
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
333 write.table(hotspot.analysis.sum, hotspot.analysis.sum.file, quote=F, sep=",", row.names=F, col.names=F, na="0")
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
334
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
335
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
336
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
337
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
338
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
339
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
340
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
341
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
342
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
343
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
344
b6f9a640e098 Uploaded
davidvanzessen
parents:
diff changeset
345
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davidvanzessen
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