IPI-class {AnnBuilder}R Documentation

Class "IPI" a sub-class of pubRepo to handle data from International Protein Index (IPI)

Description

This class is a sub-class of pubRepo that is implemented specifically to parse data from IPI (ipi.*.dat.gz)

Objects from the Class

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

Slots

srcUrl:
Object of class "character", from class "pubRepo" a character string for the surce url where data will be downloaded/processed
parser:
Object of class "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 generated
baseFile:
Object of class "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.

Extends

Class "pubRepo", directly.

Methods

parseData
signature(object = "IPI"): A method to parse a source file using a specified parser

Note

This class is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics funtionalities through R

Author(s)

Ting-Yuan Liu

References

http://www.ebi.ac.uk/IPI/IPIhelp.html

See Also

pubRepo-class

Examples

## 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)

[Package AnnBuilder version 1.8.0 Index]