R: Bacterial complete genome data from ncbi ftp site

get.ncbi {seqinr} | R Documentation

## Bacterial complete genome data from ncbi ftp site

### Description

Try to connect to ncbi ftp site to get a list of complete bacterial genomes.

### Usage

    get.ncbi(repository = "ftp://ftp.ncbi.nih.gov/genomes/Bacteria/")

### Arguments

`repository` | Where to look for data. The default value is the location of the complete bacterial genome sequences at ncbi ftp repository.

### Value

Returns a data frame which contains the following columns:

`species` | The species name as given by the corresponding folder name in the repository (e.g. Yersinia\_pestis\_KIM).
`accession` | The accession number as given by the common prefix of file names in the repository (e.g. NC\_004088).
`size.bp` | The size of the sequence in bp (e.g. 4600755).
`type` | A factor with two levels (plasmid or chromosome) temptatively deduced from the description of the sequence.

### WARNING

This function is highly dependant on ncbi ftp site conventions for which we have no control. The ftp connection apparently does not work when there is a proxy, this problem is circumvented here in a rather crude way.

### Author(s)

J.R. Lobry

### References

`citation("seqinr")`

### Examples

    ## Not run: bacteria <- get.ncbi()
    ## Not run: summary(bacteria)

[Package seqinr version 3.4-5 Index]