/usr/lib/python2.7/dist-packages/smalr/R/call_motifFinder.r is in smalr 1.0.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | pkgTest <- function(x)
{
if (!require(x,character.only = TRUE))
{
install.packages(x,dep=TRUE,repos="http://R-Forge.R-project.org")
if(!require(x,character.only = TRUE)) stop("Package not found")
}
}
pkgTest("seqinr")
args <- commandArgs(TRUE)
script<-args[1]
motif<-args[2]
mod_shift<-as.numeric(args[3])
ref<-args[4]
setwd("./")
source(script)
findMotifReadSpace(motif=motif,shift=mod_shift,genomeName=ref)
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