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### -----------------------------------------------------------------
### query the new CNEData data package
### Not exported!
#dbName = "/mnt/biggley/projects/gtan/projects/CNEr/CNErData/CNEData.sqlite"
#target = "equCab2"
#query = "canFam3"
#type = "all"
#winSize = 50
#identity = 49
#foo = queryCNEData(dbName, target, query, winSize, identity, type)
queryCNEData <- function(dbName, target, query, winSize, identity,
type=c("target", "all")
){
type <- match.arg(type)
con <- dbConnect(SQLite(), dbname=dbName)
on.exit(dbDisconnect(con))
tableName <- ifelse(target < query, paste(target, query, sep="_"),
paste(query, target, sep="_"))
tableName <- paste(tableName, identity, winSize, sep="_")
if(type == "target"){
if(target < query){
sqlCmd <- "SELECT chr1, start1, end1"
}else{
sqlCmd <- "SELECT chr2, start2, end2"
}
#}else if(type == "query"){
# if(target < query){
# sqlCmd <- "SELECT chr2, start2, end2"
# }else{
# sqlCmd <- "SELECT chr1, start1, end1"
# }
}else if(type == "all"){
if(target < query){
sqlCmd <- "SELECT chr1, start1, end1, chr2, start2, end2"
}else{
sqlCmd <- "SELECT chr2, start2, end2, chr1, start1, end1"
}
}
sqlCmd <- paste(sqlCmd, "FROM", tableName)
cne <- dbGetQuery(con, sqlCmd)
return(cne)
}
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