biofiles (version 1.0.0)

genomeRecordFromNCBI: Fetch genomes from NCBI

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.

Value

A '>gbRecord or '>gbRecordList object.

Details

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

Examples

# NOT RUN {
gbk <- genomeRecordFromNCBI(which = "bacteria/Chlamydia_muridarum", verbose = TRUE)

# }