envfascpp: Convert Fasta Files into Environment Vectors

In EnvNJ: Whole Genome Phylogenies Using Sequence Environments

Description

Converts fasta files into environment vectors

Usage

envfascpp(path, r = 10, exefile, outfile)

Arguments

path	path to the folder that contain a the file 'list.txt', which contains the names of all the fasta files to be analyzed (one per line). The fasta files must be in the same path.
r	a positive integer indicating the radius of the sequence segment considered as environment.
exefile	path to the directory containing the envfas executable.
outfile	path to, and name of, output file.

Details

This function builds and write vectors representing the species' proteome. To use this function, you must first download the source code envfas.cpp (https://bitbucket.org/jcaledo/envnj/src/master/AncillaryCode/envfas.cpp) and compile it.

Value

A txt file per fasta file analyzed. Each txt file can be read as a vector. Thus the number of lines gives the dimension of the vector.

See Also

envnj(), fastaconc()

Examples

## Not run: envfastacpp("./data_t/list.txt", 10, ".", "./MyResults")

EnvNJ documentation built on Sept. 27, 2021, 5:07 p.m.