merge_files: Merge multiple assemblies

In ArnaudDroitLab/wgs: Automate the downloading of genbank wgs

Description

Merge multiple assemblies

Usage

merge_files(n, output, dir = ".", metadata = NULL, strict = FALSE,
  force = FALSE)

Arguments

n	The names of the bacteria to download, correcponds to the organism_name column from the metadata parameter.
output	The filename to save the merged fasta.
dir	The download directory. Default: ..
metadata	The metadata file downloaded with the fetch_bacteria_metadata function. If NULL, the pre-computed metadatas will be used. Default: NULL
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, remove file if it already exists. Default: FALSE.

Value

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

Examples

## Not run: 
  merge("Campylobacter avium", output = "c_avium.fna")

## End(Not run)

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