Mercurial > repos > petrn > repeatexplorer
comparison lib/tarean/mgblast2GL.R @ 0:f6ebec6e235e draft
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| author | petrn |
|---|---|
| date | Thu, 19 Dec 2019 13:46:43 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:f6ebec6e235e |
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| 1 #!/usr/bin/env Rscript | |
| 2 ## get script dir: | |
| 3 initial.options <- commandArgs(trailingOnly = FALSE) | |
| 4 file.arg.name <- "--file=" | |
| 5 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)]) | |
| 6 script.dir <- normalizePath(dirname(script.name)) | |
| 7 fout <- commandArgs(T)[[2]] | |
| 8 | |
| 9 source(paste(script.dir, "/methods.R", sep='')) | |
| 10 suppressPackageStartupMessages (library(igraph)) | |
| 11 fin <- commandArgs(T)[[1]] | |
| 12 | |
| 13 colcls = rep("NULL", 12) | |
| 14 colcls[c(1,5,11)] = c("character","character","numeric") | |
| 15 cat("loading mgblast table\n") | |
| 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")) | |
| 17 | |
| 18 cat("creating graph\n") | |
| 19 GL = list() | |
| 20 colnames(df) = c("V1", "V2", "weight") | |
| 21 GL$G = graph.data.frame(df , directed = FALSE) | |
| 22 print(summary(GL$G)) | |
| 23 cat("calculating ogdf layouts\n") | |
| 24 try({ | |
| 25 L1 <- OGDFlayout(GL$G, alg=c("fmmm")) | |
| 26 }) | |
| 27 cat("calculating fruchterman reingold layouts\n") | |
| 28 | |
| 29 L2 = layout.fruchterman.reingold(GL$G,dim=3) | |
| 30 if (class(L1) != "try-error"){ | |
| 31 GL$L <- cbind(L1[[1]],L2) | |
| 32 }else{ | |
| 33 GL$L <- L2 | |
| 34 } | |
| 35 cat("saving output\n") | |
| 36 save(GL, file=fout) |