Nothing
getSRAinfo <-
function( in_acc, sra_con, sraType = 'sra' ) {
## note: 'litesra' has phased out
sraFile <- listSRAfile(in_acc, sra_con=sra_con, fileType=sraType, srcType='ftp')
sraFileDir <- paste(na.omit(unique(dirname(sraFile$ftp))), '/',
sep='')
file_name=NULL
file_size=NULL
file_date=NULL
require(RCurl)
opts=curlOptions(header=TRUE)
for( sraFileDir_1 in sraFileDir ) {
x <- getURL(sraFileDir_1,.opts=opts)
x1 <- strsplit(x[1], "\n")[[1]]
x2 <- sub('^.*\\s+anonymous\\s+','', x1, perl=TRUE)
file_name <-
c(file_name,
paste(sraFileDir_1, sub('^.*\\s+','', x2, perl=TRUE),
sep='') )
file_date1 =sub('^\\d+\\s{1}','', x2, perl=TRUE)
file_date <-
c(file_date,
substr(file_date1, 1,
gregexpr("\\s", file_date1, perl=TRUE)[[1]][4]-1 ) )
file_size <-
c(file_size,
ceiling(as.integer(sub('\\s+.*$','', x2, perl=TRUE)) / 1024) )
## curlPerform sometimes gives 'Access denied: 530' error
Sys.sleep(0.5)
}
file_info <-
as.data.frame(cbind('file_name'=file_name,
'size(KB)'=file_size, 'date'=file_date))
sraFileInfo <-
merge(sraFile, file_info, by.x="ftp", by.y="file_name",
all.x=TRUE)
return(sraFileInfo)
}
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