genomeRecordFromNCBI: Fetch genomes from NCBI

In biofiles: An Interface for GenBank/GenPept Flat Files

Description

## CURRENTLY BROKEN ##

Usage

genomeRecordFromNCBI(which, ignore.case = TRUE, .parse = TRUE, ...)

Arguments

which	Path to an organism on NCBI's Genomes/RefSeq FTP site. Examples would be bacteria/Acetobacter_aceti/latest_assembly_versions/GCF_002723895.1_ASM272389v1. If there are multiple matching directories the user will be prompted to choose one. If there are multiple matching gbk files the user will also be prompted to choose one or more.
ignore.case	Ignore case when matching.
.parse	if FALSE, return a character vector instead of a gbRecord object.
...	Arguments passed on to curlOptions.

Details

Retrieve genomes in GenBank format directly from NCBI's Genomes/RefSeq FTP site.

Value

A gbRecord or gbRecordList object.

Examples

## Not run: 
gbk <- genomeRecordFromNCBI(which = "bacteria/Chlamydia_muridarum", verbose = TRUE)


## End(Not run)

biofiles documentation built on May 2, 2019, 3:31 p.m.