--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/tarean/mgblast2GL.R	Thu Dec 19 10:24:45 2019 -0500
@@ -0,0 +1,36 @@
+#!/usr/bin/env Rscript
+## get script dir:
+initial.options <- commandArgs(trailingOnly = FALSE)
+file.arg.name <- "--file="
+script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
+script.dir <- normalizePath(dirname(script.name))
+fout <- commandArgs(T)[[2]]
+
+source(paste(script.dir, "/methods.R", sep=''))
+suppressPackageStartupMessages (library(igraph))
+fin <- commandArgs(T)[[1]]
+
+colcls = rep("NULL", 12)
+colcls[c(1,5,11)] = c("character","character","numeric")
+cat("loading mgblast table\n")
+df = read.table(pipe(paste("cut -f1,5,11 ",fin)), sep="\t",comment.char="", as.is=TRUE, header= FALSE, colClasses = c("character","character","numeric"))
+
+cat("creating graph\n")
+GL = list()
+colnames(df) =  c("V1", "V2", "weight")
+GL$G = graph.data.frame(df , directed = FALSE)
+print(summary(GL$G))
+cat("calculating ogdf layouts\n")
+try({
+    L1 <- OGDFlayout(GL$G, alg=c("fmmm"))
+})
+cat("calculating fruchterman reingold layouts\n")
+
+L2 = layout.fruchterman.reingold(GL$G,dim=3)
+if (class(L1) != "try-error"){
+    GL$L <- cbind(L1[[1]],L2)
+}else{
+    GL$L <- L2
+}
+cat("saving output\n")
+save(GL, file=fout)