genomeFTP: Retrieve genome FTP URL
In YulongNiu/ProGenome: A package for processing prokaryotic genomes

Description Usage Arguments Details Value Author(s) References Examples

Get genomic information NCBI FTP url

GetSpeFtpUrl(KEGGSpe, database = "GenBank")

KEGGSpe2NCBIAss(KEGGSpe)

LatestAss(assNum)

AutoSpeFtpUrl(KEGGSpe)

ListFileFtpUrl(ftpUrl)

read.gff(filePath, isurl = FALSE, isgz = FALSE)

`KEGGSpe`	A KEGG species ID
`database`	"GenBank", "RefSeq", or c("GenBank", "RefSeq").
`assNum`	assembly number or the genome GenBank/RefSeq number
`ftpUrl`	FTP url that can be the output of function getFtpUrl()
`filePath`	A local file path or a web url.
`isurl`	Whether a url (TRUE) or not (FALSE).
`isgz`	Whether a gzfile (TRUE) or not (FALSE).

GetSpeFtpUrl(): get the FTP url storing genome information from GenBank or RefSeq database. This function is mainly used to get the species genome assembly information.

AutoSpeFtpUrl(): automatically choose the FTP url. This function trys the RefSeq at first and then GenBank.

ListFtpFileUrl(): list the file download FTP urls.

read.gff(): read in a raw gff file (or gz file) from the local disk or web url.

FTP url.

KEGGSpe2NCBIAss(): NCBI assembly ID

LatestAss(): latest assembly number

AutoSpeFtpUrl(): RefSeq or GenBank FTP url

ListFileFtpUrl(): a list of download FTP urls

read.gff(): a table of raw gff/feature_table file

Yulong Niu niuylscu@gmail.com

How to read in gz files into R from FTP URL https://stackoverflow.com/questions/9548630/read-gzipped-csv-directly-from-a-url-in-r

## E. coli genome GenBank and RefSeq FTP
ecoliUrl <- GetSpeFtpUrl('eco', c('GenBank', 'RefSeq'))
## automatically choose FTP
ecoliAutoUrl <- AutoSpeFtpUrl('eco')
## list E. coli FTP files
ecoliFiles <- ListFileFtpUrl(ecoliAutoUrl)

## read in gff file
gffUrl <- ecoliFiles[grepl('gff', ecoliFiles)]
ecoligff <- read.gff(gffUrl, isurl = TRUE, isgz = TRUE)

## read in the dra (Deinococcus radiodurans R1) gff gz file in local disk
gzPath <- system.file('extdata', 'dra.gff.gz', package = 'ProGenome')
dragff <- read.gff(gzPath, isurl = FALSE, isgz = TRUE)

## read in the dra gff file in local disk
gffPath <- system.file('extdata', 'dra.gff', package = 'ProGenome')
dragff <- read.gff(gzPath, isurl = FALSE, isgz = FALSE)

## Not run: 
## read in dra gff files through FTP URL
draUrl <- AutoSpeFtpUrl('dra')
dragff <- ListFileFtpUrl(draUrl)
dragff <- read.gff(dragff[grepl('gff', dragff)])

## End(Not run)