Commit 67656044 authored by Aroon Chande's avatar Aroon Chande

Plot skeleton for protein predictions, for real this time

parent 0a2b5b99
Pipeline #34 passed with stage
in 24 seconds
......@@ -26,12 +26,7 @@ plotGff <- function(outdir){
plot_gene_map(dna_segs = dna, annotations = annot)
}
plotSkel <- function(outdir){
genplotdata <-
paste(
'/home/blast/prediction_server/server/gff.pl -fasta '
,outdir,'/prots.faa', sep="")
system(genplotdata)
filelist = dir(outdir, pattern = "*.ptt")
filelist = dir('/home/blast/prediction_server/server/skel/', pattern = "*.ptt")
dna <- list()
annot <- list()
for (i in 1:length(filelist)) {
......@@ -63,12 +58,14 @@ shinyServer(function(input, output, session) {
if (seqCond == 'protein' &
predCond == 'pred' &
input$submit != 0L & !is.null(input$fastaFile)) {
outdir = substr(input$fastaFile$datapath, 1, nchar(input$fastaFile$datapath) - 1)
cpProt <- paste('cp ', input$fastaFile$datapath, ' ', outdir, '/prots.faa', sep="")
system(cpProt)
sed <- paste("sed -i 's/ #.*.//g' ",outdir,"/prots.faa", sep="")
system(sed)
t6pred(outdir)
plotSkel()
}
else if (predCond == 'pred' &
seqCond == 'genomic' &
......
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