random_dna_seq: Shuffle a sequence with a kept kmer distribution

In jkruppa/virDisco: Modules for a viral detection pipeline

Description

The function shuffles a given sequence and keeps a given k distribution

Usage

random_dna_seq(inFile, outFile, k, n = 1, clean = TRUE, tmpDir,
  fasta_formatter = NULL, fasta_uShuffle = NULL)

Arguments

inFile	File path to the fasta file to be shuffled
outFile	File path to the out dir
k	Kept k for the shuffling (k < 25)
n	Number of produced shuffle sequences per sequence [default = 1]
clean	Should everthing removed [default = TRUE]
tmpDir	Where to save temp files
fasta_formatter	File path to the fasta formatter executables
fasta_uShuffle	File path to the fasta uShuffle executables

Details

The function calls uShuffle, which can only handle fasta files without a linebreak. Therefore, the program formatter removes all linebreaks from the fasta file beforehand. Than uShuffle shuffles the sequence by keeping a distrubtion of kmer's given k.

Value

Null

Author(s)

Jochen Kruppa

jkruppa/virDisco documentation built on May 3, 2019, 7:05 p.m.