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1 #!/usr/bin/env Rscript
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2
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3 args <- commandArgs(trailingOnly = TRUE)
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4
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5 #this programs normalizes a saint input file based on the spectral counts of all preys
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6
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7 d = read.delim(args[1], header=T, sep="\t", as.is=T)
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8
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9 baitn = 1
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10 curr_bait <- d$Bait[1]
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11 s <- vector()
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12 s[1] = 0
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13 for(i in 1:length(d$Bait)){
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14 if(curr_bait != d$Bait[i]){
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15 baitn <- baitn + 1
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16 curr_bait <- d$Bait[i]
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17 s[baitn] <- d$AvgSpec[i]
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18 }
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19 else{
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20 s[baitn] <- s[baitn] + d$AvgSpec[i]
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21 }
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22 }
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23
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24 med.s = median(s)
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25 s = s / med.s
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26
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27 d_n <- d
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28 baitn = 1
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29 curr_bait <- d_n$Bait[1]
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30 for(i in 1:length(d_n$Bait)){
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31 if(curr_bait != d_n$Bait[i]){
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32 baitn <- baitn + 1
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33 curr_bait <- d_n$Bait[i]
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34 d_n$AvgSpec[i] <- d_n$AvgSpec[i]/s[baitn]
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35 }
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36 else{
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37 d_n$AvgSpec[i] <- d_n$AvgSpec[i]/s[baitn]
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38 }
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39 }
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40
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41 #print normalized data to file
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42
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43 write.table(d_n, file = "norm_saint.txt", sep="\t", quote=F, row.names=F)
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44
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