Nothing
pBaseBuilder_DB <- function(baseMapType = c("sp","trembl","ipi","refseq"), organism,
prefix, pkgPath, version, author
) {
## Build annotation data packages for proteins in primary protein database.
##
## baseMapType - a character string that can be either "sp", "trembl", "ipi"
## or "refseq" to indicate which protein database will be used.
## "sp": UniProtKB/Swiss-Prot
## "trembl": UniProtKB/TrEMBL
## "ipi": International Protein Index (IPI)
## Homo sapiens, HUMAN
## Mus musculus, MOUSE
## Rattus norvegicus, RAT
## Danio rerio, DANRE
## Bos taurus, BOVIN
## Gallus gallus, CHICK
## Arabidopsis thaliana, ARATH
## "refseq": NCBI Reference Sequence
## Homo sapiens, H_sapiens
## Mus musculus, M_musculus
## Rattus norvegicus, R_norvegicus
## Danio rerio, D_rerio
## Bos taurus, B_taurus
## Xenopus tropicalis, X_tropicalis
##
##
## organism - a character string for the name of the organism of
## concern. [eg: Homo sapiens]
##
## prefix - the prefix of the data package to be built (e.g. "hsaSP"). The name
## of builded package is prefix+".db".
##
## pkgPath - a character string for the full path of an existing
## directory where the built backage will be stored.
##
## version - a character string for the version number.
##
## author - a list with named elements "authors" containing a character
## vector of author names and "maintainer" containing the complete
## character string for the maintainer field, for example, "Jane
## Doe <jdoe@doe.com>".
##
## Copyright 2008, Hong Li, all rights reserved.
##
if(any(c(missing(baseMapType), missing(prefix), missing(pkgPath),
missing(organism), missing(version), missing(author),
is.null(baseMapType), is.null(prefix), is.null(pkgPath),
is.null(organism), is.null(version), is.null(author)))){
stop(paste("Parameters baseMapType, prefix, pkgPath, organism, ",
"version, or author can not be missing or NULL",
sep = ""))
}
type <- match.arg(baseMapType)
if( !any(type==c("sp","trembl","ipi","refseq")) ){
stop("Parameter baseMapType is not correct, must be sp,trembl,ipi or refseq")
}
if( type=="refseq" & !any(organism==c("Homo sapiens","Mus musculus",
"Rattus norvegicus","Danio rerio","Bos taurus","Xenopus tropicalis"))){
stop( paste("Parameter organism \"", "\" is not supported for RefSeq
database, must be Homo sapiens, Mus musculus, Rattus norvegicus,
Danio rerio, Bos taurus or Xenopus tropicalis." , sep=organism) )
}
if( type=="ipi" & !any(organism==c("Homo sapiens","Mus musculus",
"Rattus norvegicus","Danio rerio","Bos taurus","Gallus gallus",
"Arabidopsis thaliana"))){
stop( paste("Parameter organism \"", "\" is not supported for IPI database,
must be Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio,
Bos taurus, Gallus gallus or Arabidopsis thaliana." , sep=organism) )
}
pkgName = paste(prefix,"db",sep=".")
srcUrls <- getSrcUrl(type, organism = organism)
built <- getSrcBuilt(type, organism = organism)
# create annotation package, and write data into "*.sqlite" file
createEmptyDPkg(pkgName, pkgPath, force = TRUE,
folders = c("man", "R", paste("inst","extdata",sep=.Platform$file.sep) ))
drv <- dbDriver("SQLite")
outputFile <- file.path(pkgPath, pkgName, paste("inst",
"extdata", sep=.Platform$file.sep), paste(prefix, "sqlite", sep="."))
db <- dbConnect(drv, outputFile)
# write data
writeData_DB(type, srcUrls, db, organism)
repList <- getRepList_DB(organism, type, srcUrls, built, pkgName)
writeMeta_DB(db, repList)
writeManAnno_DB(pkgName, pkgPath, version, author, repList)
countFields <- data.frame(c("IPIAC","PFAM","PATH","INTERPRO"),
c("ipi_id","ipi_id","ipi_id","ipi_id"),
c("ipiac","pfam","path","interpro"))
buildMapCounts(db,countFields)
dbDisconnect(db)
}
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