inst/extdata/runEnrichPep.R

In WubingZhang/PhageR: Functions for phage display data analysis

args <-  commandArgs(T)
# args[1]: Project name.
# args[2]: output directory.
# args[3]: kmer.
# args[4]: length of peptide.
# args[5]: Number of controls.
# args[6]: Number of treatments.
# args[7]: Fastq file list, should be ctls and treatments.
suppressPackageStartupMessages(library(PhageR))
enrich.pep(fastqs = args[7:length(args)], ctl = 1:as.integer(args[5]),
           trt = (as.integer(args[5])+1):(as.integer(args[5])+as.integer(args[6])),
           proj = args[1], outdir = args[2], peplen = as.integer(args[4]),
           kmer = as.integer(args[3]), nperm=1000, distrBase = FALSE, distrAA = TRUE,
           refseq_fa = "~/Jobs/Project/XunBaihui/_Data/6_PhageDisplay/Mmu_Proteosome/UP000000589_10090.fasta")
# try(blastEnrichedKmer(paste0(args[2], "/", args[1], "_", args[3], "mer_summary.txt"),
#                       prefix = args[1], outdir = args[2]), TRUE)
# blastRes_files = list.files(args[2], paste0(args[3], "mer_blastRes.txt"), full.names = TRUE)
# if(length(blastRes_files)>0){
#   sampleNames = gsub(paste0(".*", args[1], "_|", paste0(args[3], "mer_blastRes.txt")), "", blastRes_files)
#   try(eProteinView(blastRes_files, sampleNames, args[2]))
# }