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

In cstubben/genomes2: Genome sequencing project metadata

Description

Read files from the NCBI genomes FTP

Usage

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

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

Value

a Biostring or GRanges object

Note

The genomes FTP site was updated on Dec 2, 2015 ftp://ftp.ncbi.nlm.nih.gov/genomes/README.txt and the default directory is now genomes/archive/old_refseq/Bacteria

Author(s)

Chris Stubben

See Also

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

Examples

## Not run: 


org<-"Burkholderia_pseudomallei_K96243_uid57733"
read.ncbi.ftp(org)         # Protein and rna tables
read.ncbi.ftp(org, "gff")  # GFF
read.ncbi.ftp(org, "fna")  # Genome sequences

read.ncbi.ftp(org, "Prod") # Prodigal annotations
read.ncbi.ftp(org, "Glim") # Glimmer


## End(Not run)

cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.