genomes (version 2.16.0)

read.ncbi.ftp: Read files from the NCBI genomes FTP

Description

Read files from the NCBI genomes FTP

Usage

read.ncbi.ftp(org, filePattern = "ptt$|rnt$", ftp = "genomes/ASSEMBLY_BACTERIA", ...)

Arguments

org

organism directory (new FTP requires species and refseq assembly)

filePattern

load files matching a specific pattern, default is protein and rna tables

ftp

name of base FTP directory

...

other options passed to read functions

Value

Details

This function reads files in the genomes FTP and loads sequence files (faa=protein, fna=genone, ffn=gene, frn=rna) using Biostring functions or converts coordinate files (gff, ptt, rnt, GeneMarkHMM, Glimmer, Prodigal) to GRanges

See Also

read.gff, read.ptt, read.genemark, read.glimmer, read.prodigal

Examples

## Not run: 
# 
# #NEW FTP uses species and RefSeq assembly
# 
# org <- "Burkholderia_pseudomallei/GCF_000011545"
# read.ncbi.ftp(org)         # Protein and rna tables
# read.ncbi.ftp(org, "gff")  # GFF
# read.ncbi.ftp(org, "fna")  # Genome sequences
# 
# # OLD genomes FTP uses strain and reseq project ID
# # ALSO includes prodigal, genemark and glimmer predictions (not on new site)
# 
# org <- "Burkholderia_pseudomallei_K96243_uid57733"
# read.ncbi.ftp(org, "Prod", ftp = "genomes/Bacteria") # Prodigal annotations
# read.ncbi.ftp(org, "Glim", ftp = "genomes/Bacteria") # Glimmer
# 
# ## End(Not run)