RASTtogbk: Write RAST files to Genbank formats OrthoMCL Analysis

In corinsexton/MAGNAMWAR: A Pipeline for Meta-Genome Wide Association

Description

Useful for reformating RAST files to GBK format

Usage

RASTtoGBK(input_fasta, input_reference, out_name_path)

Arguments

input_fasta	path to input fasta file
input_reference	path to a .csv file; it should be downloaded from RAST as excel format, saved as a .csv (saved as the tab-delimited version has compatibility problems)
out_name_path	name and path of the file to write to

Examples

lfrc_fasta <- system.file('extdata', 'RASTtoGBK//lfrc.fasta', package='MAGNAMWAR')
lfrc_reference <- system.file('extdata', 'RASTtoGBK//lfrc_lookup.csv', package='MAGNAMWAR')
lfrc_path <- system.file('extdata', 'RASTtoGBK//lfrc_out.fasta', package='MAGNAMWAR')

RASTtoGBK(lfrc_fasta,lfrc_reference,lfrc_path)

corinsexton/MAGNAMWAR documentation built on May 13, 2019, 10:51 p.m.