Mercurial > repos > czouaoui > gc_cover_data
changeset 20:50809ff03c17 draft
Uploaded
| author | czouaoui |
|---|---|
| date | Wed, 16 May 2018 10:11:00 -0400 |
| parents | 3e855db19775 |
| children | 514a2b9d8e2e |
| files | gc_cover_data/getGCCoverData.R |
| diffstat | 1 files changed, 16 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gc_cover_data/getGCCoverData.R Wed May 16 10:11:00 2018 -0400 @@ -0,0 +1,16 @@ +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) +sessionInfo() +library(Biostrings) +sessionInfo() +# test if there is at least one argument: if not, return an error +if (length(args) != 3) { + stop("At least 3 arguments must be supplied (Fasta file, Coverage file, Fasta file name)", call.=FALSE) +} + +seqString <- read.fasta(args[1], seqonly=TRUE) +sequence <- DNAString(seqString[[1]]) +covData <- scan(args[2], integer(), sep =",", skip = 1) +seqName <- strsplit(args[3], '[.].*') + +save(sequence, covData, seqName, file="gcCover.RData")