Mercurial > repos > rhpvorderman > shm_csr

annotate sequence_overview.r @ 2:72d68e2e1fd3 draft

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"planemo upload commit a8565b413cbe0ef70bc22994ecdd48b400ba6185"
author rhpvorderman
date Fri, 05 Nov 2021 14:43:13 +0000
parents 64d74ba01a7c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
101
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
102 sequence.id.page="by_id.html"
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
103
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
104 for(i in 1:nrow(dat)){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
105
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
106 ca1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGA1", IDs$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
107 ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGA2", IDs$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
108
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
109 cg1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG1", IDs$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
110 cg2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG2", IDs$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
111 cg3 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG3", IDs$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
112 cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG4", IDs$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
113
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
114 cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGM", IDs$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
115
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
116 ce = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGE", IDs$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
117
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
118 un = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^unmatched", IDs$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
119
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
120 allc = rbind(ca1, ca2, cg1, cg2, cg3, cg4, cm, ce, un)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
121
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
122 ca1.n = nrow(ca1)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
123 ca2.n = nrow(ca2)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
124
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
125 cg1.n = nrow(cg1)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
126 cg2.n = nrow(cg2)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
127 cg3.n = nrow(cg3)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
128 cg4.n = nrow(cg4)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
129
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
130 cm.n = nrow(cm)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
131
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
132 ce.n = nrow(ce)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
133
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
134 un.n = nrow(un)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
135
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
136 classes = c(ca1.n, ca2.n, cg1.n, cg2.n, cg3.n, cg4.n, cm.n, ce.n, un.n)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
137
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
138 classes.sum = sum(classes)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
139
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
140 if(classes.sum == 1){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
141 single.sequences = single.sequences + 1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
142 next
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
143 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
144
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
145 if(un.n == classes.sum){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
146 unmatched = unmatched + 1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
147 next
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
148 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
149
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
150 classes.no.un = classes[-length(classes)]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
151
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
152 in.classes = sum(classes.no.un > 0)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
153
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
154 matched = matched + in.classes #count in how many subclasses the sequence occurs.
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
155
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
156 if(any(classes == classes.sum)){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
157 multiple.in.one = multiple.in.one + 1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
158 } else if (un.n > 0) {
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
159 some.unmatched = some.unmatched + 1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
160 } else {
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
161 in.multiple = in.multiple + 1
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
162 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
163
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
164 id = as.numeric(dat[i,"seq_conc"])
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
165
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
166 functionality = paste(unique(allc[,"Functionality"]), collapse=",")
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
167
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
168 by.id.row = c()
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
169
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
170 if(ca1.n > 0){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
171 cat(tbl(ca1), file=paste("IGA1_", id, ".html", sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
172 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
173
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
174 if(ca2.n > 0){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
175 cat(tbl(ca2), file=paste("IGA2_", id, ".html", sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
176 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
177
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
178 if(cg1.n > 0){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
179 cat(tbl(cg1), file=paste("IGG1_", id, ".html", sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
180 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
181
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
182 if(cg2.n > 0){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
183 cat(tbl(cg2), file=paste("IGG2_", id, ".html", sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
184 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
185
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
186 if(cg3.n > 0){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
187 cat(tbl(cg3), file=paste("IGG3_", id, ".html", sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
188 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
189
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
190 if(cg4.n > 0){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
191 cat(tbl(cg4), file=paste("IGG4_", id, ".html", sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
192 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
193
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
194 if(cm.n > 0){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
195 cat(tbl(cm), file=paste("IGM_", id, ".html", sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
196 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
197
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
198 if(ce.n > 0){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
199 cat(tbl(ce), file=paste("IGE_", id, ".html", sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
200 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
201
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
202 if(un.n > 0){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
203 cat(tbl(un), file=paste("un_", id, ".html", sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
204 }
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
205
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
206 ca1.html = make.link(id, "IGA1", ca1.n)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
207 ca2.html = make.link(id, "IGA2", ca2.n)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
208
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
209 cg1.html = make.link(id, "IGG1", cg1.n)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
210 cg2.html = make.link(id, "IGG2", cg2.n)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
211 cg3.html = make.link(id, "IGG3", cg3.n)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
212 cg4.html = make.link(id, "IGG4", cg4.n)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
213
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
214 cm.html = make.link(id, "IGM", cm.n)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
215
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
parents:
diff changeset
216 ce.html = make.link(id, "IGE", ce.n)
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217
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218 un.html = make.link(id, "un", un.n)
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diff changeset
219
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
rhpvorderman
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220 #extra columns
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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221 ca.n = ca1.n + ca2.n
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222
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223 cg.n = cg1.n + cg2.n + cg3.n + cg4.n
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224
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diff changeset
225 #in.classes
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226
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diff changeset
227 in.ca.cg = (ca.n > 0 & cg.n > 0)
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228
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229 in.ca.cg.cm = (ca.n > 0 & cg.n > 0 & cm.n > 0)
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230
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231 in.ca.cg.ce = (ca.n > 0 & cg.n > 0 & ce.n > 0)
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232
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233 in.ca.cg.cm.ce = (ca.n > 0 & cg.n > 0 & cm.n > 0 & ce.n > 0)
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234
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235 in.ca1.ca2 = (ca1.n > 0 & ca2.n > 0)
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236
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237 in.cg1.cg2 = (cg1.n > 0 & cg2.n > 0)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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238 in.cg1.cg3 = (cg1.n > 0 & cg3.n > 0)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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239 in.cg1.cg4 = (cg1.n > 0 & cg4.n > 0)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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240 in.cg2.cg3 = (cg2.n > 0 & cg3.n > 0)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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241 in.cg2.cg4 = (cg2.n > 0 & cg4.n > 0)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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242 in.cg3.cg4 = (cg3.n > 0 & cg4.n > 0)
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243
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244 in.cg1.cg2.cg3 = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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245 in.cg2.cg3.cg4 = (cg2.n > 0 & cg3.n > 0 & cg4.n > 0)
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246 in.cg1.cg2.cg4 = (cg1.n > 0 & cg2.n > 0 & cg4.n > 0)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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247 in.cg1.cg3.cg4 = (cg1.n > 0 & cg3.n > 0 & cg4.n > 0)
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248
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249 in.cg.all = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0 & cg4.n > 0)
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250
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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)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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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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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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254
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255
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256
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257 cat(tr(rw), file=main.html, append=T)
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258
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259
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260 for(i in 1:nrow(allc)){ #generate html by id
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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261 html = make.link(id, allc[i,"best_match"], allc[i,"Sequence.ID"])
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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262 cat(paste(html, "<br />"), file=sequence.id.page, append=T)
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263 }
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264 }
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265
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266 cat("</table>", file=main.html, append=T)
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267
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268 print(paste("Single sequences:", single.sequences))
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269 print(paste("Sequences in multiple subclasses:", in.multiple))
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270 print(paste("Multiple sequences in one subclass:", multiple.in.one))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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271 print(paste("Matched with unmatched:", some.unmatched))
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272 print(paste("Count that should match 'matched' sequences:", matched))
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273
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274 #ACGT overview
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275
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276 #NToverview = merged[!grepl("^unmatched", merged$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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277 NToverview = merged
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278
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279 if(empty.region.filter == "leader"){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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280 NToverview$seq = paste(NToverview$FR1.IMGT.seq, NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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281 } else if(empty.region.filter == "FR1"){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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282 NToverview$seq = paste(NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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283 } else if(empty.region.filter == "CDR1"){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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284 NToverview$seq = paste(NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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285 } else if(empty.region.filter == "FR2"){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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286 NToverview$seq = paste(NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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287 }
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288
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289 NToverview$A = nchar(gsub("[^Aa]", "", NToverview$seq))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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290 NToverview$C = nchar(gsub("[^Cc]", "", NToverview$seq))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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291 NToverview$G = nchar(gsub("[^Gg]", "", NToverview$seq))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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292 NToverview$T = nchar(gsub("[^Tt]", "", NToverview$seq))
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293
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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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295
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296 #NToverview = rbind(NToverview, NTsum)
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297
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298 NTresult = data.frame(nt=c("A", "C", "T", "G"))
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299
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300 for(clazz in gene.classes){
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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301 print(paste("class:", clazz))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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302 NToverview.sub = NToverview[grepl(paste("^", clazz, sep=""), NToverview$best_match),]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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303 print(paste("nrow:", nrow(NToverview.sub)))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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304 new.col.x = c(sum(NToverview.sub$A), sum(NToverview.sub$C), sum(NToverview.sub$T), sum(NToverview.sub$G))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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305 new.col.y = sum(new.col.x)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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306 new.col.z = round(new.col.x / new.col.y * 100, 2)
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307
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308 tmp = names(NTresult)
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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309 NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z))
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310 names(NTresult) = c(tmp, paste(clazz, c("x", "y", "z"), sep=""))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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311 }
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312
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313 NToverview.tmp = NToverview[,c("Sequence.ID", "best_match", "seq", "A", "C", "G", "T")]
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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314
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315 names(NToverview.tmp) = c("Sequence.ID", "best_match", "Sequence of the analysed region", "A", "C", "G", "T")
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316
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317 write.table(NToverview.tmp, NToverview.file, quote=F, sep="\t", row.names=F, col.names=T)
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318
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319 NToverview = NToverview[!grepl("unmatched", NToverview$best_match),]
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320
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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321 new.col.x = c(sum(NToverview$A), sum(NToverview$C), sum(NToverview$T), sum(NToverview$G))
64d74ba01a7c "planemo upload commit 78d1fae87dbcf490e49a9f99e7a06de7328e16d4"
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322 new.col.y = sum(new.col.x)
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323 new.col.z = round(new.col.x / new.col.y * 100, 2)
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325 tmp = names(NTresult)
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326 NTresult = cbind(NTresult, data.frame(new.col.x, new.col.y, new.col.z))
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327 names(NTresult) = c(tmp, paste("all", c("x", "y", "z"), sep=""))
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328
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329 names(hotspot.analysis.sum) = names(NTresult)
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330
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331 hotspot.analysis.sum = rbind(hotspot.analysis.sum, NTresult)
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332
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333 write.table(hotspot.analysis.sum, hotspot.analysis.sum.file, quote=F, sep=",", row.names=F, col.names=F, na="0")
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334
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335
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343
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