augustus: wrapper to run AUGUSTUS

In dongzhuoer/mcapomorphy: Molecular Classfication based on amino acid apomorphy

Description

wrapper to run AUGUSTUS

Usage

augustus(species, input, output = NULL, args = "", ...)

Arguments

species	string. an identifier for the species model to use, such as 'chicken'
input	string. path to the input file, which contains the gene sequence(s) in fasta format.
output	string. path to the output file. if NULL output is writen into standard output
args	character. additional parameters passed on to AUGUSTUS
...	other parameters passed on to system2(), from stdout to the end

Value

result of system2() or NULL if input doesn't exist

Examples

## Not run: 
    augustus('human', 'software/augustus/examples/example.fa');
    augustus('human', 'software/augustus/examples/hsackI10.fa.gz')

    augustus('human', 'software/augustus/examples/example.fa', 'test.gff');

## End(Not run)

dongzhuoer/mcapomorphy documentation built on Jan. 9, 2020, 3:28 a.m.