inst/extdata/PeptideQC.R

In WubingZhang/PhageR: Functions for phage display data analysis

args <-  commandArgs(T)
# args[1]: pattern of fastqs
# args[2]: fastq directory.
# args[3]: out directory
# args[4]: length of peptide.

library(PhageR)
tmp = c(".fq.gz", "./", "./", "12")
if(length(args)<5){
  args = c(args, tmp[(length(args)+1):5])
}
pattern = args[1]
fqdir = args[2]
outdir = args[3]
peplen = as.integer(args[4])

message("Pattern of fastq files: ", pattern,
        "\nPath to fastq files: ", fqdir,
        "\nOutput directory: ", outdir,
        "\nLength of peptides: ", peplen)

SeqDistribution(fq_pattern = pattern, fqdir = fqdir, outdir = outdir, peplen = peplen)