download_files: Download fasta files

In ArnaudDroitLab/wgs: Automate the downloading of genbank wgs

Description

Download the _cds_from_genomic.fna.gz files for a list of bacteria

Usage

download_files(n, metadata = NULL, dir = ".", merge = NULL,
  strict = TRUE, force = FALSE, verbose = FALSE, check_md5 = FALSE)

Arguments

n	The names of the bacteria to download, correcponds to the organism_name column from the metadata parameter.
metadata	The metadata file downloaded with the fetch_bacteria_metadata function. If NULL, the pre-computed metadatas will be used. Default: NULL
dir	The output directory. Default: ..
strict	If TRUE, the names must be identical to the organism_name column of the metadata object (by default, it's the bacteria object). Otherwise, partial match will be allowed and the matchning will not be case sensitive. Default: TRUE.
force	If TRUE, the file will be downloaded even if it is already present in the dir/fna directory. Default: FALSE.
verbose	Print details of the downloading process. Default: FALSE.
check_md5	Check the md5 value of the files that are already downloaded. Default: FALSE.

Details

This script will download all the _cds_from_genomic.fna.gz based on a list of bacteria names.

The results will be saved in the 'codedir/fna/ directory.

To avoid redownloading the same files over and over, this function will check by default if the file is already present with the correct md5sum before downloading.

Value

Invisibly return the subset of metadata that was selected to download.

Examples

## Not run: 
  download_files("Campylobacter_avium")

## End(Not run)

ArnaudDroitLab/wgs documentation built on June 21, 2019, 1:51 p.m.