download_refseq: Download RefSeq genome libraries

In wevanjohnson/animalcules.preprocess: This package contains tools and functions for preprocessing microbiome data

Description

This function will automatically download RefSeq genome libraries in a .fasta format from the specified kingdom. The function will first download the summary report at: ftp://ftp.ncbi.nlm.nih.gov/genomes/**kingdom**/overview.txt, and then use this file to download genomes and combine them in a single compressed or uncompressed .fasta file.

Usage

download_refseq(kingdom, reference = TRUE, representative = FALSE,
  compress = TRUE)

Arguments

kingdom	Select the kingdom taxonomy to download. Options are 'archaea', 'bacteria', 'fungi', 'invertebrate', 'plant', 'protozoa', 'vertibrate', 'vertibrate_other', 'viral'
reference	Download only RefSeq reference genomes? Defaults to TRUE. Automatically set to TURE if representative is TRUE
representative	Download only RefSeq representative genomes? Defaults to FALSE. If TRUE, reference is automatically set at TRUE
compress	Compress the output .fasta file? Defaults to TRUE

Value

Returns a .fasta or .fasta.gz file of the desired RefSeq genomes. This file is named after the kindom selectd and saved to the current directory (e.g. 'bacteria.fasta.gz'). Currently, this function also returns a .fasta file formatted for PathoScope as well (e.g. 'bacteria.pathoscope.fasta.gz'), but this will soon be retired.

Examples

## Download all RefSeq reference bacterial genomes
download_refseq('bacteria')

## Download all RefSeq representative viral genomes
download_refseq( 'viral', representative = TRUE )

## Download all RefSeq viral genomes
download_refseq( 'viral', reference = FALSE ) 

wevanjohnson/animalcules.preprocess documentation built on May 11, 2019, 8:26 p.m.