## File: get.ncbi.Rd

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r-cran-seqinr 3.4-5-2
 1234567891011121314151617181920212223242526272829303132333435363738394041 \name{get.ncbi} \alias{get.ncbi} \alias{ncbi.fna.url} \alias{ncbi.ptt.url} \alias{ncbi.stats} \alias{ncbi.gbk.url} \title{ 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{ \item{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: \item{species}{The species name as given by the corresponding folder name in the repository (\emph{e.g.} Yersinia\_pestis\_KIM).} \item{accession}{The accession number as given by the common prefix of file names in the repository (\emph{e.g.} NC\_004088).} \item{size.bp}{The size of the sequence in bp (\emph{e.g.} 4600755).} \item{type}{A factor with two levels (plasmid or chromosome) temptatively deduced from the description of the sequence.} } \references{ \code{citation("seqinr")} } \author{J.R. Lobry} \section{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. } \examples{ \dontrun{bacteria <- get.ncbi()} \dontrun{summary(bacteria)} } \keyword{utilities}