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1 #!/usr/bin/env Rscript
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2 ## get script dir:
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3 initial.options <- commandArgs(trailingOnly = FALSE)
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4 file.arg.name <- "--file="
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5 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
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6 script.dir <- normalizePath(dirname(script.name))
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7 fout <- commandArgs(T)[[2]]
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8
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9 source(paste(script.dir, "/methods.R", sep=''))
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10 suppressPackageStartupMessages (library(igraph))
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11 fin <- commandArgs(T)[[1]]
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12
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13 colcls = rep("NULL", 12)
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14 colcls[c(1,5,11)] = c("character","character","numeric")
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15 cat("loading mgblast table\n")
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16 df = read.table(pipe(paste("cut -f1,5,11 ",fin)), sep="\t",comment.char="", as.is=TRUE, header= FALSE, colClasses = c("character","character","numeric"))
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17
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18 cat("creating graph\n")
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19 GL = list()
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20 colnames(df) = c("V1", "V2", "weight")
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21 GL$G = graph.data.frame(df , directed = FALSE)
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22 print(summary(GL$G))
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23 cat("calculating ogdf layouts\n")
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24 try({
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25 L1 <- OGDFlayout(GL$G, alg=c("fmmm"))
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26 })
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27 cat("calculating fruchterman reingold layouts\n")
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28
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29 L2 = layout.fruchterman.reingold(GL$G,dim=3)
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30 if (class(L1) != "try-error"){
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31 GL$L <- cbind(L1[[1]],L2)
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32 }else{
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33 GL$L <- L2
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34 }
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35 cat("saving output\n")
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36 save(GL, file=fout)
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