Nothing
R/sqlForge_schemaGen.R
In AnnotationForge: Tools for building SQLite-based annotation data packages
Defines functions
makeFooPkg
analyzeVacuumDisconnect
generate.schema
available.chipdbschemas
available.dbschemas
available.db0pkgs
popYEASTNCBIDB
popXENOPUSDB
popXENOPUSCHIPDB
popANOPHELESDB
popRHESUSDB
popRHESUSCHIPDB
popCHIMPDB
popCHICKENDB
popCHICKENCHIPDB
popPIGDB
popPIGCHIPDB
popWORMDB
popWORMCHIPDB
popBOVINEDB
popBOVINECHIPDB
popCANINEDB
popCANINECHIPDB
popECOLIDB
popECOLICHIPDB
popZEBRAFISHDB
popZEBRAFISHCHIPDB
popMALARIADB
popYEASTDB
popYEASTCHIPDB
popFLYDB
popFLYCHIPDB
popARABIDOPSISDB
popARABIDOPSISCHIPDB
popRATDB
popRATCHIPDB
popMOUSEDB
popMOUSECHIPDB
popHUMANDB
popHUMANCHIPDB
Documented in
available.chipdbschemas
available.db0pkgs
available.dbschemas
popBOVINECHIPDB
popBOVINEDB
popCANINECHIPDB
popCANINEDB
popCHICKENCHIPDB
popCHICKENDB
popECOLICHIPDB
popECOLIDB
popFLYCHIPDB
popFLYDB
popHUMANCHIPDB
popHUMANDB
popMALARIADB
popMOUSECHIPDB
popMOUSEDB
popPIGCHIPDB
popPIGDB
popRATCHIPDB
popRATDB
popWORMCHIPDB
popWORMDB
popYEASTDB
popYEASTNCBIDB
popZEBRAFISHCHIPDB
popZEBRAFISHDB
#presently this is the formula for HUMANCHIP_DB
popHUMANCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_human.sqlite", package="human.db0"),
chipSrc = system.file("extdata", "chipsrc_human.sqlite", package="human.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="human","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendOmim(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for HUMAN_DB
popHUMANDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_human.sqlite", package="human.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="human","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendOmim(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendUCSCGenes(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for MOUSECHIP_DB
popMOUSECHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_mouse.sqlite", package="mouse.db0"),
chipSrc = system.file("extdata", "chipsrc_mouse.sqlite", package="mouse.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="mouse","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendMGI(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for MOUSE_DB
popMOUSEDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_mouse.sqlite", package="mouse.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="mouse","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
## appendUCSCGenes(db, subStrs=subStrs, printSchema=printSchema)
appendMGI(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for RATCHIP_DB
popRATCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_rat.sqlite", package="rat.db0"),
chipSrc = system.file("extdata", "chipsrc_rat.sqlite", package="rat.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="rat","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for RAT_DB
popRATDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_rat.sqlite", package="rat.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="rat","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for ARABIDOPSISCHIP_DB
popARABIDOPSISCHIPDB <- function(affy,
prefix,
fileName="myFile.txt",
chipMapSrc = system.file("extdata", "chipmapsrc_arabidopsis.sqlite", package="arabidopsis.db0"),
chipSrc = system.file("extdata", "chipsrc_arabidopsis.sqlite", package="arabidopsis.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
#This function needs some more work if we want it to be able to have other people use it
#specifically the code for the next line must be generalized.
getMapForArabidopsisChipPkg(affy = affy,
fileName = fileName,
pkgName = prefix,
chipMapSrc = chipMapSrc,
outputDir = outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="arabidopsis","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendArabidopsisGenes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisEntrezGenes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisProbes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisGeneInfo(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAraCyc(db, subStrs=subStrs, printSchema=printSchema)
appendAraCycEnzyme(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyArabidopsisProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for ARABIDOPSIS_DB
popARABIDOPSISDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_arabidopsis.sqlite", package="arabidopsis.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="TAIR","org"="arabidopsis","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
dbGetQuery(db, "CREATE TABLE probe_map (probe_id TEXT, gene_id TEXT, accession TEXT);")
dbGetQuery(db, "CREATE TABLE metadata (name VARCHAR(80) PRIMARY KEY, value VARCHAR(255) );")
dbGetQuery(db, paste("INSERT INTO metadata VALUES ('PKGNAME', '", prefix, "');", sep="", collapse=""))
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendArabidopsisGenes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisEntrezGenes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisGeneInfo(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendAraCyc(db, subStrs=subStrs, printSchema=printSchema)
appendAraCycEnzyme(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
makeGOViews(db)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for FLYCHIP_DB
popFLYCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_fly.sqlite", package="fly.db0"),
chipSrc = system.file("extdata", "chipsrc_fly.sqlite", package="fly.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="fly","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBase(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBaseCG(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for FLY_DB
popFLYDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_fly.sqlite", package="fly.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="fly","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBase(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBaseCG(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBaseProt(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for YEASTCHIP_DB
#Like popARABIDOPSISCHIDB(), popYEASTCHIPDB() is only really ready to run with affy chips though we can update this in future as needed.
popYEASTCHIPDB <- function(affy,
prefix,
fileName,
chipSrc = system.file("extdata", "chipsrc_yeast.sqlite", package="yeast.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
#the following function makes a decision based on the value in the affy parameter:
getMapForYeastChipPkg(affy, fileName=fileName, pkgName=prefix, outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="yeast","cntrTab"="sgd", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendYeastSGD(db, subStrs=subStrs, printSchema=printSchema)
appendYeastProbes(db, subStrs=subStrs, printSchema=printSchema)
appendYeastOrphanMeta(db, subStrs=subStrs)
appendYeastChromosomeFeatures(db, subStrs=subStrs, printSchema=printSchema)
appendYeastAlias(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyYeastProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for YEAST_DB
popYEASTDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_yeast.sqlite", package="yeast.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="sgd","coreID"="systematic_name","suffix"="ORF","org"="yeast","cntrTab"="sgd", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
dbGetQuery(db, "CREATE TABLE probe_map (probe_id TEXT, gene_id TEXT, accession TEXT);")
dbGetQuery(db, "CREATE TABLE metadata (name VARCHAR(80) PRIMARY KEY, value VARCHAR(255) );")
dbGetQuery(db, paste("INSERT INTO metadata VALUES ('PKGNAME', '", prefix, "');", sep="", collapse=""))
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendYeastSGD(db, subStrs=subStrs, printSchema=printSchema)
appendYeastOrphanMeta(db, subStrs=subStrs)
appendYeastChromosomeFeatures(db, subStrs=subStrs, printSchema=printSchema)
appendYeastAlias(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendYeastPfam(db, subStrs=subStrs, printSchema=printSchema)
appendYeastSmart(db, subStrs=subStrs, printSchema=printSchema)
appendYeastInterpro(db, subStrs=subStrs, printSchema=printSchema)
appendYeastRejectORF(db, subStrs=subStrs, printSchema=printSchema)
appendYeastGene2Systematic(db, subStrs=subStrs, printSchema=printSchema)
##Append the 3 tables that come from the NCBI data
appendExternalEG(db, subStrs=subStrs, printSchema=printSchema) ##needed to cover case where genes table is not central...
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for MALARIA_DB
popMALARIADB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_malaria.sqlite", package="malaria.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="ORF","org"="malaria","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for ZEBRAFISHCHIP_DB
popZEBRAFISHCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_zebrafish.sqlite", package="zebrafish.db0"),
chipSrc = system.file("extdata", "chipsrc_zebrafish.sqlite", package="zebrafish.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="zebrafish","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendZfin(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for ZEBRAFISH_DB
popZEBRAFISHDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_zebrafish.sqlite", package="zebrafish.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="zebrafish","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendZfin(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for ECOLICHIP_DB
popECOLICHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_ecoliK12.sqlite", package="ecoliK12.db0"),
chipSrc = system.file("extdata", "chipsrc_ecoliK12.sqlite", package="ecoliK12.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="ecoli","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for ECOLI_DB
popECOLIDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_ecoliK12.sqlite", package="ecoliK12.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="ecoli","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for CANINECHIP_DB
popCANINECHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_canine.sqlite", package="canine.db0"),
chipSrc = system.file("extdata", "chipsrc_canine.sqlite", package="canine.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="canine","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for CANINE_DB
popCANINEDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_canine.sqlite", package="canine.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="canine","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for BOVINECHIP_DB
popBOVINECHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_bovine.sqlite", package="bovine.db0"),
chipSrc = system.file("extdata", "chipsrc_bovine.sqlite", package="bovine.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="bovine","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for BOVINE_DB
popBOVINEDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_bovine.sqlite", package="bovine.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="bovine","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for WORMCHIP_DB
popWORMCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_worm.sqlite", package="worm.db0"),
chipSrc = system.file("extdata", "chipsrc_worm.sqlite", package="worm.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="worm","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendWormbase(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for WORM_DB
popWORMDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_worm.sqlite", package="worm.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="worm","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendWormbase(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for PIGCHIP_DB
popPIGCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_pig.sqlite", package="pig.db0"),
chipSrc = system.file("extdata", "chipsrc_pig.sqlite", package="pig.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="pig","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for PIG_DB
popPIGDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_pig.sqlite", package="pig.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="pig","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for CHICKENCHIP_DB
popCHICKENCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_chicken.sqlite", package="chicken.db0"),
chipSrc = system.file("extdata", "chipsrc_chicken.sqlite", package="chicken.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="chicken","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for CHICKEN_DB
popCHICKENDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_chicken.sqlite", package="chicken.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="chicken","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
##This is the formula for CHIMP_DB
popCHIMPDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_chimp.sqlite", package="chimp.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="chimp","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
## appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for RHESUSCHIP_DB
popRHESUSCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_rhesus.sqlite", package="rhesus.db0"),
chipSrc = system.file("extdata", "chipsrc_rhesus.sqlite", package="rhesus.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="rhesus","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
#appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
#appendPfam(db, subStrs=subStrs, printSchema=printSchema)
#appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for RHESUS_DB
popRHESUSDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_rhesus.sqlite", package="rhesus.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="rhesus","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
## appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for ANOPHELES_DB
popANOPHELESDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_anopheles.sqlite", package="anopheles.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="anopheles","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
## appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for XENOPUSCHIP_DB
popXENOPUSCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_xenopus.sqlite", package="xenopus.db0"),
chipSrc = system.file("extdata", "chipsrc_xenopus.sqlite", package="xenopus.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="xenopus","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
## appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
## appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
## appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for XENOPUS_DB
popXENOPUSDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_xenopus.sqlite", package="xenopus.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="xenopus","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
## appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
## appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
## appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for YEASTNCBI_DB
popYEASTNCBIDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_yeastNCBI.sqlite", package="yeastNCBI.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="human","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendOmim(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
## appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
## appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendYeastNCBILocusTags(db, subStrs=subStrs, printSchema=printSchema)
appendYeastNCBISGD(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
available.db0pkgs <- function()
{
url <-
"http://bioconductor.org/packages/release/data/annotation/src/contrib"
pkgs <- available.packages(url)[, "Package"]
pkgs <- pkgs[substr(pkgs, nchar(pkgs)-3, nchar(pkgs)) == ".db0"]
names(pkgs) <- NULL
pkgs
}
available.dbschemas <- function(){
##need a generic path
path = system.file(package="AnnotationDbi")
path = paste(path,"/DBschemas/schemas_1.0", sep = "")
list = list.files(path)
list = list[grep("_DB.sql", list)]
list = gsub(".sql","",list)
list
}
available.chipdbschemas <- function(){
list = available.dbschemas()
list = list[grep("CHIP_DB", list)]
list
}
##Generate a schema for an installed package. Why installed? Because I will
##be the primary user of this, and it is good for me to have to install at
##least one example of each type of supported package while testing. Also,
##this means that these things will always be in a standardized place which
##will make it easier to script this stuff. Also, this will ensure that
##updating the schemas and bumping AnnotationDbi will be one of the last
##things I do. This function ONLY works with SQLite DBs (all we use)
generate.schema <- function(name = "HUMANCHIP_DB", pkg = "hgu95av2.db", path = "." ){
pkgname = sub(".db",".sqlite",pkg)
dbFile = system.file("extdata",pkgname,package=pkg)
drv = dbDriver("SQLite")
con = dbConnect(drv, dbname=dbFile)
sql = "SELECT * FROM sqlite_master;"
res = dbGetQuery(con, sql)
##Now we have to format it nicely...
res = res[,5]
res = res[!is.na(res)]
##Add semicolons to the end of the elements in res
res = gsub("$",";",res,perl=TRUE)
##Insert some lines right before the end index:
indNums = grep("INDEX",res) #number to insert lines before.
nonIndNums = grep("INDEX",res, invert=TRUE)
##Tnen use paste to insert the comments
indexComment = "\n-- Explicit index creation on the referencing column of all the foreign keys.\n-- Note that this is only needed for SQLite: PostgreSQL and MySQL create those\n-- indexes automatically."
res = c(res[nonIndNums],indexComment,res[indNums])
##Then write it out to a file.
write(res, file = paste( name,".sql", sep=""))
##Then disconnect (so there won't be limits on how many times we can call this)
dbDisconnect(con)
}
analyzeVacuumDisconnect <- function(drv,outputDir,prefix){
db <- dbConnect(drv, dbname = file.path(outputDir,
paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, "ANALYZE;")
dbGetQuery(db, "VACUUM;")
dbDisconnect(db)
}
#Test formula to just see if my generic functions work:
makeFooPkg <- function(){
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="human","cntrTab"="genes", "prefix"="pkgFoo", "outDir"=".")
drv <- dbDriver("SQLite")
db <- dbConnect(drv,dbname=paste(subStrs[["prefix"]],".sqlite", sep=""))
createCntrTableGeneric(db, subStrs, printSchema=FALSE, table="genes", field="gene_id",fileName="fakeyIDs.txt")
dbDisconnect(db)
db <- dbConnect(drv,dbname=paste(subStrs[["prefix"]],".sqlite", sep=""))
appendProbesGeneric(db, subStrs, printSchema=FALSE, table="probes", matchID="gene_id", field="probe_id", fileName="fakeyProbes.txt", mapCounts="PROBECOUNT")
dbDisconnect(db)
db <- dbConnect(drv,dbname=paste(subStrs[["prefix"]],".sqlite", sep=""))
appendGeneric(db, subStrs, printSchema=FALSE, table="refseq", matchID="gene_id", field="refseq_id", fileName="fakeyRefSeqs.txt", mapCounts="FOOCOUNT")
dbDisconnect(db)
}
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Defines functions makeFooPkg analyzeVacuumDisconnect generate.schema available.chipdbschemas available.dbschemas available.db0pkgs popYEASTNCBIDB popXENOPUSDB popXENOPUSCHIPDB popANOPHELESDB popRHESUSDB popRHESUSCHIPDB popCHIMPDB popCHICKENDB popCHICKENCHIPDB popPIGDB popPIGCHIPDB popWORMDB popWORMCHIPDB popBOVINEDB popBOVINECHIPDB popCANINEDB popCANINECHIPDB popECOLIDB popECOLICHIPDB popZEBRAFISHDB popZEBRAFISHCHIPDB popMALARIADB popYEASTDB popYEASTCHIPDB popFLYDB popFLYCHIPDB popARABIDOPSISDB popARABIDOPSISCHIPDB popRATDB popRATCHIPDB popMOUSEDB popMOUSECHIPDB popHUMANDB popHUMANCHIPDB
Documented in available.chipdbschemas available.db0pkgs available.dbschemas popBOVINECHIPDB popBOVINEDB popCANINECHIPDB popCANINEDB popCHICKENCHIPDB popCHICKENDB popECOLICHIPDB popECOLIDB popFLYCHIPDB popFLYDB popHUMANCHIPDB popHUMANDB popMALARIADB popMOUSECHIPDB popMOUSEDB popPIGCHIPDB popPIGDB popRATCHIPDB popRATDB popWORMCHIPDB popWORMDB popYEASTDB popYEASTNCBIDB popZEBRAFISHCHIPDB popZEBRAFISHDB
#presently this is the formula for HUMANCHIP_DB
popHUMANCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_human.sqlite", package="human.db0"),
chipSrc = system.file("extdata", "chipsrc_human.sqlite", package="human.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="human","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendOmim(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for HUMAN_DB
popHUMANDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_human.sqlite", package="human.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="human","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendOmim(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendUCSCGenes(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for MOUSECHIP_DB
popMOUSECHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_mouse.sqlite", package="mouse.db0"),
chipSrc = system.file("extdata", "chipsrc_mouse.sqlite", package="mouse.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="mouse","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendMGI(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for MOUSE_DB
popMOUSEDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_mouse.sqlite", package="mouse.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="mouse","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
## appendUCSCGenes(db, subStrs=subStrs, printSchema=printSchema)
appendMGI(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for RATCHIP_DB
popRATCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_rat.sqlite", package="rat.db0"),
chipSrc = system.file("extdata", "chipsrc_rat.sqlite", package="rat.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="rat","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for RAT_DB
popRATDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_rat.sqlite", package="rat.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="rat","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for ARABIDOPSISCHIP_DB
popARABIDOPSISCHIPDB <- function(affy,
prefix,
fileName="myFile.txt",
chipMapSrc = system.file("extdata", "chipmapsrc_arabidopsis.sqlite", package="arabidopsis.db0"),
chipSrc = system.file("extdata", "chipsrc_arabidopsis.sqlite", package="arabidopsis.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
#This function needs some more work if we want it to be able to have other people use it
#specifically the code for the next line must be generalized.
getMapForArabidopsisChipPkg(affy = affy,
fileName = fileName,
pkgName = prefix,
chipMapSrc = chipMapSrc,
outputDir = outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="arabidopsis","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendArabidopsisGenes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisEntrezGenes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisProbes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisGeneInfo(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAraCyc(db, subStrs=subStrs, printSchema=printSchema)
appendAraCycEnzyme(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyArabidopsisProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for ARABIDOPSIS_DB
popARABIDOPSISDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_arabidopsis.sqlite", package="arabidopsis.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="TAIR","org"="arabidopsis","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
dbGetQuery(db, "CREATE TABLE probe_map (probe_id TEXT, gene_id TEXT, accession TEXT);")
dbGetQuery(db, "CREATE TABLE metadata (name VARCHAR(80) PRIMARY KEY, value VARCHAR(255) );")
dbGetQuery(db, paste("INSERT INTO metadata VALUES ('PKGNAME', '", prefix, "');", sep="", collapse=""))
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendArabidopsisGenes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisEntrezGenes(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendArabidopsisGeneInfo(db, subStrs=subStrs, printSchema=printSchema) ##Arabidopsis requires a custom function.
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendAraCyc(db, subStrs=subStrs, printSchema=printSchema)
appendAraCycEnzyme(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
makeGOViews(db)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for FLYCHIP_DB
popFLYCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_fly.sqlite", package="fly.db0"),
chipSrc = system.file("extdata", "chipsrc_fly.sqlite", package="fly.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="fly","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBase(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBaseCG(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for FLY_DB
popFLYDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_fly.sqlite", package="fly.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="fly","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBase(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBaseCG(db, subStrs=subStrs, printSchema=printSchema)
appendFlyBaseProt(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for YEASTCHIP_DB
#Like popARABIDOPSISCHIDB(), popYEASTCHIPDB() is only really ready to run with affy chips though we can update this in future as needed.
popYEASTCHIPDB <- function(affy,
prefix,
fileName,
chipSrc = system.file("extdata", "chipsrc_yeast.sqlite", package="yeast.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
#the following function makes a decision based on the value in the affy parameter:
getMapForYeastChipPkg(affy, fileName=fileName, pkgName=prefix, outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="yeast","cntrTab"="sgd", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendYeastSGD(db, subStrs=subStrs, printSchema=printSchema)
appendYeastProbes(db, subStrs=subStrs, printSchema=printSchema)
appendYeastOrphanMeta(db, subStrs=subStrs)
appendYeastChromosomeFeatures(db, subStrs=subStrs, printSchema=printSchema)
appendYeastAlias(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyYeastProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for YEAST_DB
popYEASTDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_yeast.sqlite", package="yeast.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="sgd","coreID"="systematic_name","suffix"="ORF","org"="yeast","cntrTab"="sgd", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
dbGetQuery(db, "CREATE TABLE probe_map (probe_id TEXT, gene_id TEXT, accession TEXT);")
dbGetQuery(db, "CREATE TABLE metadata (name VARCHAR(80) PRIMARY KEY, value VARCHAR(255) );")
dbGetQuery(db, paste("INSERT INTO metadata VALUES ('PKGNAME', '", prefix, "');", sep="", collapse=""))
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendYeastSGD(db, subStrs=subStrs, printSchema=printSchema)
appendYeastOrphanMeta(db, subStrs=subStrs)
appendYeastChromosomeFeatures(db, subStrs=subStrs, printSchema=printSchema)
appendYeastAlias(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendYeastPfam(db, subStrs=subStrs, printSchema=printSchema)
appendYeastSmart(db, subStrs=subStrs, printSchema=printSchema)
appendYeastInterpro(db, subStrs=subStrs, printSchema=printSchema)
appendYeastRejectORF(db, subStrs=subStrs, printSchema=printSchema)
appendYeastGene2Systematic(db, subStrs=subStrs, printSchema=printSchema)
##Append the 3 tables that come from the NCBI data
appendExternalEG(db, subStrs=subStrs, printSchema=printSchema) ##needed to cover case where genes table is not central...
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for MALARIA_DB
popMALARIADB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_malaria.sqlite", package="malaria.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="ORF","org"="malaria","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for ZEBRAFISHCHIP_DB
popZEBRAFISHCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_zebrafish.sqlite", package="zebrafish.db0"),
chipSrc = system.file("extdata", "chipsrc_zebrafish.sqlite", package="zebrafish.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="zebrafish","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendZfin(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for ZEBRAFISH_DB
popZEBRAFISHDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_zebrafish.sqlite", package="zebrafish.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="zebrafish","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendZfin(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for ECOLICHIP_DB
popECOLICHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_ecoliK12.sqlite", package="ecoliK12.db0"),
chipSrc = system.file("extdata", "chipsrc_ecoliK12.sqlite", package="ecoliK12.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="ecoli","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for ECOLI_DB
popECOLIDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_ecoliK12.sqlite", package="ecoliK12.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="ecoli","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for CANINECHIP_DB
popCANINECHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_canine.sqlite", package="canine.db0"),
chipSrc = system.file("extdata", "chipsrc_canine.sqlite", package="canine.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="canine","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for CANINE_DB
popCANINEDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_canine.sqlite", package="canine.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="canine","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for BOVINECHIP_DB
popBOVINECHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_bovine.sqlite", package="bovine.db0"),
chipSrc = system.file("extdata", "chipsrc_bovine.sqlite", package="bovine.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="bovine","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for BOVINE_DB
popBOVINEDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_bovine.sqlite", package="bovine.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="bovine","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for WORMCHIP_DB
popWORMCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_worm.sqlite", package="worm.db0"),
chipSrc = system.file("extdata", "chipsrc_worm.sqlite", package="worm.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="worm","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendWormbase(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for WORM_DB
popWORMDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_worm.sqlite", package="worm.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="worm","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendWormbase(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for PIGCHIP_DB
popPIGCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_pig.sqlite", package="pig.db0"),
chipSrc = system.file("extdata", "chipsrc_pig.sqlite", package="pig.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="pig","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for PIG_DB
popPIGDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_pig.sqlite", package="pig.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="pig","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for CHICKENCHIP_DB
popCHICKENCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_chicken.sqlite", package="chicken.db0"),
chipSrc = system.file("extdata", "chipsrc_chicken.sqlite", package="chicken.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="chicken","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for CHICKEN_DB
popCHICKENDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_chicken.sqlite", package="chicken.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="chicken","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
appendPfam(db, subStrs=subStrs, printSchema=printSchema)
appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
##This is the formula for CHIMP_DB
popCHIMPDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_chimp.sqlite", package="chimp.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="chimp","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
## appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#presently this is the formula for RHESUSCHIP_DB
popRHESUSCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_rhesus.sqlite", package="rhesus.db0"),
chipSrc = system.file("extdata", "chipsrc_rhesus.sqlite", package="rhesus.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="rhesus","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
#appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
#appendPfam(db, subStrs=subStrs, printSchema=printSchema)
#appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for RHESUS_DB
popRHESUSDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_rhesus.sqlite", package="rhesus.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="rhesus","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
## appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for ANOPHELES_DB
popANOPHELESDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_anopheles.sqlite", package="anopheles.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="anopheles","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
## appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for XENOPUSCHIP_DB
popXENOPUSCHIPDB <- function(affy,
prefix,
fileName,
chipMapSrc = system.file("extdata", "chipmapsrc_xenopus.sqlite", package="xenopus.db0"),
chipSrc = system.file("extdata", "chipsrc_xenopus.sqlite", package="xenopus.db0"),
metaDataSrc,
otherSrc=character(0),
baseMapType="gbNRef",
outputDir=".",
printSchema=FALSE){
if(affy==TRUE){
getMapForBiocChipPkg(
csvFileName=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
else if(affy==FALSE){
getMapForOtherChipPkg(
filePath=fileName,
pkgName=prefix,
chipMapSrc=chipMapSrc,
chipSrc=chipSrc,
otherSrc=otherSrc,
baseMapType=baseMapType,
outputDir=outputDir
)
}
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="xenopus","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="ChipDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendProbes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
## appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
## appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
## appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
appendPostMeta(db, subStrs=subStrs)
simplifyProbes(db, subStrs=subStrs)
dropRedundantTables(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for XENOPUS_DB
popXENOPUSDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_xenopus.sqlite", package="xenopus.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="xenopus","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
## appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
## appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl2NCBI(db, subStrs=subStrs, printSchema=printSchema)
## appendNCBI2Ensembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
#This is the formula for YEASTNCBI_DB
popYEASTNCBIDB <- function(prefix,
chipSrc = system.file("extdata", "chipsrc_yeastNCBI.sqlite", package="yeastNCBI.db0"),
metaDataSrc,
outputDir=".",
printSchema=FALSE){
makeUniversalMapping(pkgName=prefix,
chipSrc=chipSrc,
outputDir=outputDir)
#define the substitution needed by the support functions.
subStrs <- c("coreTab"="genes","coreID"="gene_id","suffix"="EG","org"="human","cntrTab"="genes", "prefix"=prefix, "outDir"=outputDir, "Db_type"="OrgDb")
drv <- dbDriver("SQLite")
db <- dbConnect(drv, dbname = file.path(outputDir, paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, paste("ATTACH DATABASE '",chipSrc,"' AS anno;",sep="") )
appendPreMeta(db, subStrs=subStrs, printSchema=printSchema, metaDataSrc=metaDataSrc)
appendGenes(db, subStrs=subStrs, printSchema=printSchema)
appendGeneInfo(db, subStrs=subStrs, printSchema=printSchema)
appendChromosomes(db, subStrs=subStrs, printSchema=printSchema)
appendAccessions(db, subStrs=subStrs, printSchema=printSchema)
## appendCytogenicLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendOmim(db, subStrs=subStrs, printSchema=printSchema)
appendRefseq(db, subStrs=subStrs, printSchema=printSchema)
appendPubmed(db, subStrs=subStrs, printSchema=printSchema)
## appendUnigene(db, subStrs=subStrs, printSchema=printSchema)
appendChrlengths(db, subStrs=subStrs, printSchema=printSchema)
appendGO(db, subStrs=subStrs, printSchema=printSchema)
appendGOALL(db, subStrs=subStrs, printSchema=printSchema)
appendKEGG(db, subStrs=subStrs, printSchema=printSchema)
appendEC(db, subStrs=subStrs, printSchema=printSchema)
## appendChromsomeLocs(db, subStrs=subStrs, printSchema=printSchema)
## appendPfam(db, subStrs=subStrs, printSchema=printSchema)
## appendProsite(db, subStrs=subStrs, printSchema=printSchema)
appendAlias(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsembl(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblProt(db, subStrs=subStrs, printSchema=printSchema)
## appendEnsemblTrans(db, subStrs=subStrs, printSchema=printSchema)
appendYeastNCBILocusTags(db, subStrs=subStrs, printSchema=printSchema)
appendYeastNCBISGD(db, subStrs=subStrs, printSchema=printSchema)
appendUniprot(db, subStrs=subStrs, printSchema=printSchema)
makeGOViews(db)
appendPostMeta(db, subStrs=subStrs)
dbDisconnect(db)
analyzeVacuumDisconnect(drv,outputDir,prefix)
}
available.db0pkgs <- function()
{
url <-
"http://bioconductor.org/packages/release/data/annotation/src/contrib"
pkgs <- available.packages(url)[, "Package"]
pkgs <- pkgs[substr(pkgs, nchar(pkgs)-3, nchar(pkgs)) == ".db0"]
names(pkgs) <- NULL
pkgs
}
available.dbschemas <- function(){
##need a generic path
path = system.file(package="AnnotationDbi")
path = paste(path,"/DBschemas/schemas_1.0", sep = "")
list = list.files(path)
list = list[grep("_DB.sql", list)]
list = gsub(".sql","",list)
list
}
available.chipdbschemas <- function(){
list = available.dbschemas()
list = list[grep("CHIP_DB", list)]
list
}
##Generate a schema for an installed package. Why installed? Because I will
##be the primary user of this, and it is good for me to have to install at
##least one example of each type of supported package while testing. Also,
##this means that these things will always be in a standardized place which
##will make it easier to script this stuff. Also, this will ensure that
##updating the schemas and bumping AnnotationDbi will be one of the last
##things I do. This function ONLY works with SQLite DBs (all we use)
generate.schema <- function(name = "HUMANCHIP_DB", pkg = "hgu95av2.db", path = "." ){
pkgname = sub(".db",".sqlite",pkg)
dbFile = system.file("extdata",pkgname,package=pkg)
drv = dbDriver("SQLite")
con = dbConnect(drv, dbname=dbFile)
sql = "SELECT * FROM sqlite_master;"
res = dbGetQuery(con, sql)
##Now we have to format it nicely...
res = res[,5]
res = res[!is.na(res)]
##Add semicolons to the end of the elements in res
res = gsub("$",";",res,perl=TRUE)
##Insert some lines right before the end index:
indNums = grep("INDEX",res) #number to insert lines before.
nonIndNums = grep("INDEX",res, invert=TRUE)
##Tnen use paste to insert the comments
indexComment = "\n-- Explicit index creation on the referencing column of all the foreign keys.\n-- Note that this is only needed for SQLite: PostgreSQL and MySQL create those\n-- indexes automatically."
res = c(res[nonIndNums],indexComment,res[indNums])
##Then write it out to a file.
write(res, file = paste( name,".sql", sep=""))
##Then disconnect (so there won't be limits on how many times we can call this)
dbDisconnect(con)
}
analyzeVacuumDisconnect <- function(drv,outputDir,prefix){
db <- dbConnect(drv, dbname = file.path(outputDir,
paste(prefix,".sqlite", sep="")) )
dbGetQuery(db, "ANALYZE;")
dbGetQuery(db, "VACUUM;")
dbDisconnect(db)
}
#Test formula to just see if my generic functions work:
makeFooPkg <- function(){
subStrs <- c("coreTab"="probes","coreID"="probe_id","suffix"="PROBE","org"="human","cntrTab"="genes", "prefix"="pkgFoo", "outDir"=".")
drv <- dbDriver("SQLite")
db <- dbConnect(drv,dbname=paste(subStrs[["prefix"]],".sqlite", sep=""))
createCntrTableGeneric(db, subStrs, printSchema=FALSE, table="genes", field="gene_id",fileName="fakeyIDs.txt")
dbDisconnect(db)
db <- dbConnect(drv,dbname=paste(subStrs[["prefix"]],".sqlite", sep=""))
appendProbesGeneric(db, subStrs, printSchema=FALSE, table="probes", matchID="gene_id", field="probe_id", fileName="fakeyProbes.txt", mapCounts="PROBECOUNT")
dbDisconnect(db)
db <- dbConnect(drv,dbname=paste(subStrs[["prefix"]],".sqlite", sep=""))
appendGeneric(db, subStrs, printSchema=FALSE, table="refseq", matchID="gene_id", field="refseq_id", fileName="fakeyRefSeqs.txt", mapCounts="FOOCOUNT")
dbDisconnect(db)
}
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