envfascpp {EnvNJ} R Documentation

## Convert Fasta Files into Environment Vectors

### 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.

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