fasta.cutter: Cuts pieces of a fixed length and a random position for all...
In GuillemSalazar/FastaUtils:

Description Usage Arguments Value Author(s) Examples

View source: R/FastaUtils_functions.R

This function cuts pieces of sequences of a fixed length ('read.length') either by sampling randomly a multi-fasta file or by selecting an equal number of pieces from each sequence within a multi-fasta file.

fasta.cutter(
  infile = NULL,
  sampling.type = "none",
  total.reads = NULL,
  read.length = NULL,
  file.out = NULL,
  replacement = FALSE,
  meanlog = 0,
  sdlog = 1
)

`infile`	Multi-Fasta file.
`sampling.type`	Sampling type: select a fixed pieces from each sequence ('none', default), performs a uniform random sampling ('uniform') or a sampling based on a lognormal distribution. In the first case the total number of pieces has to be multiple of the number of sequences.
`total.reads`	Total number of pieces.
`read.length`	Length of te pieces to be cut.
`file.out`	Path to output file.
`replacement`	Logical for using or not (default) sampling of sequences with replacement. Only applies if 'sampling.type=T'.
`meanlog, sdlog`	mean and standard deviation of the distribution on the log scale with default values of 0 and 1 respectively.

Writes a fasta file with the selected sequences and a tab-delimites file with the sequence name and the start and end position of the cut. This file gets the 'file.out' names and adds '.info' at the end.

Guillem Salazar <salazar@icm.csic.es>

1	fasta.cutter(infile="http://greengenes.lbl.gov/Data/JD_Tutorial/UnAligSeq24606.txt",sampling.type="uniform",file.out="out.fasta",total.reads=15,read.length=20)