File: make_seqLogo.Rscript

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transdecoder 5.7.1-2
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#!/usr/bin/env Rscript

args<-commandArgs(TRUE)

if (length(args) == 0) {
    stop("require param: motif.+.pwm")
}

dat_filename = args[1]

library(seqLogo)

data = read.table(dat_filename, header=T, row.names=1)

data = data[,c('A', 'C', 'G', 'T')]

motif = t(data)

motif = sweep(motif, 2, colSums(motif), '/')

p = makePWM(motif)

pdf( paste0(dat_filename, ".seqLogo.pdf"))

seqLogo(p)


dev.off()