IPI-class {AnnBuilder} | R Documentation |
This class is a sub-class of pubRepo that is implemented specifically to parse data from IPI (ipi.*.dat.gz)
Objects can be created by calls of the form new("IPI", ...)
.
A constructor (IPI) is available and should be used to instatiate
objects of IPI
srcUrl
:"character", from class
"pubRepo"
a character string for the surce url where data
will be downloaded/processedparser
:"character", from class
"pubRepo"
a character string for the name of the file
containing a segment of perl code with instructions on how the
source data will be processed and output be generatedbaseFile
:"character", from
class "pubRepo"
a character string for the name of the gzipped file
that contains data from IPI ftp site. For example,
ipi.HUMAN.dat.gz is the file for human, and ipi.MOUSE.dat.gz is
for mouse, etc.
Class "pubRepo"
, directly.
signature(object = "IPI")
: A method to parse
a source file using a specified parserThis class is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics funtionalities through R
Ting-Yuan Liu
http://www.ebi.ac.uk/IPI/IPIhelp.html
## Not run: ## create IPI class ipi <- IPI(srcUrl="ftp://ftp.ebi.ac.uk/pub/databases/IPI/current/", organism = "human") ## Parse ipi.HUMAN.dat.gz from IPI ftp site tmpFile <- loadFromUrl(paste(srcUrls(ipi),baseFile(ipi)), sep="") system("grep "//" ") con <- file(tmpFile, "r") tmpRead <- readLines(con, n=200) endSymbol <- grep("//", tmpRead) tmpRead <- tmpRead[1:endSymbol[length(endSymbol)]] file <- tempfile() writeLines(tmpRead, file) system(paste("mv ", file, " ", tempdir(), "/ipi.tiny.dat", sep="")) system(paste("gzip ", tempdir(), "/ipi.tiny.dat", sep="")) ipiParser(ipiData=paste(tempdir(), "/ipi.tiny.dat.gz", sep=""), fromWeb=FALSE) ## End(Not run)