Nothing
R/metaseqr.query.R
In metaseqR: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
Defines functions
get.ucsc.credentials
get.ucsc.query
get.ucsc.tbl.tpl
get.ucsc.tabledef
get.ucsc.dbl
Documented in
get.ucsc.credentials
get.ucsc.dbl
get.ucsc.query
get.ucsc.tabledef
get.ucsc.tbl.tpl
#' Download annotation from UCSC servers, according to organism and source
#'
#' Directly downloads UCSC and RefSeq annotation files from UCSC servers to be
#' used with metaseqR. This functionality is used when the package RMySQL is not
#' available for some reason, e.g. Windows machines.
#'
#' @param org one of metaseqR supported organisms.
#' @param type either \code{"gene"} or \code{"exon"}.
#' @param refdb one of \code{"ucsc"} or \code{"refseq"} to use the UCSC or RefSeq
#' annotation sources respectively.
#' @return A data frame with annotation elements.
#' @export
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.file <- get.ucsc.file("hg18","gene","ucsc")
#'}
get.ucsc.dbl <- function(org,type,refdb="ucsc") {
type <- tolower(type[1])
org <- tolower(org[1])
refdb <- tolower(refdb[1])
check.text.args("type",type,c("gene","exon"))
check.text.args("org",org,c("hg18","hg19","hg38","mm9","mm10","rn5","dm3",
"dm6","danrer7","pantro4","susscr3","tair10"),multiarg=FALSE)
check.text.args("refdb",refdb,c("ucsc","refseq"))
if (!require(RSQLite))
stopwrap("R package RSQLite is required to use annotation from UCSC!")
http.base <- paste("http://hgdownload.soe.ucsc.edu/goldenPath/",
get.ucsc.organism(org),"/database/",sep="")
table.defs <- get.ucsc.tabledef(org,type,refdb,"fields")
file.list <- vector("list",length(table.defs))
names(file.list) <- names(table.defs)
for (n in names(file.list))
file.list[[n]] <- paste(http.base,n,".txt.gz",sep="")
# Fill the fields for each table
drv <- dbDriver("SQLite")
db.tmp <- tempfile()
con <- dbConnect(drv,dbname=db.tmp)
#disp(" Defining tables for temporary SQLite ",refdb," ",org," ",
# type," subset database")
#for (n in names(file.list)) {
# disp(" Creating table ",n,"\n")
# dbSendQuery(con,table.defs[[n]])
#}
disp(" Retrieving tables for temporary SQLite ",refdb," ",org," ",type,
" subset database")
for (n in names(file.list)) {
disp(" Retrieving table ",n)
download.file(file.list[[n]],file.path(tempdir(),
paste(n,".txt.gz",sep="")),quiet=TRUE)
if (.Platform$OS.type == "unix")
system(paste("gzip -df",file.path(tempdir(),
paste(n,".txt.gz",sep=""))))
else
unzip(file.path(tempdir(),paste(n,".txt.gz",sep="")))
sql.df <- read.delim(file.path(tempdir(),paste(n,".txt",sep="")),
row.names=NULL,header=FALSE,strip.white=TRUE)
names(sql.df) <- table.defs[[n]]
dbWriteTable(con,n,sql.df,row.names=FALSE)
}
dbDisconnect(con)
return(db.tmp)
}
#' Get SQLite UCSC table defintions, according to organism and source
#'
#' Creates a list of UCSC Genome Browser database tables and their SQLite
#' definitions with the purpose of creating a temporary SQLite database to be
#' used used with metaseqR. This functionality is used when the package RMySQL
#' is not available for some reason, e.g. Windows machines.
#'
#' @param org one of metaseqR supported organisms.
#' @param type either \code{"gene"} or \code{"exon"}.
#' @param refdb one of \code{"ucsc"} or \code{"refseq"} to use the UCSC or RefSeq
#' annotation sources respectively.
#' @return A list with SQLite table definitions.
#' @export
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.tabledefs <- get.ucsc.tables("hg18","gene","ucsc")
#'}
get.ucsc.tabledef <- function(org,type,refdb="ucsc",what="queries") {
type <- tolower(type[1])
org <- tolower(org[1])
refdb <- tolower(refdb[1])
what <- tolower(what[1])
check.text.args("type",type,c("gene","exon"))
check.text.args("org",org,c("hg18","hg19","hg38","mm9","mm10","rn5","dm3",
"dm6","danrer7","pantro4","susscr3","tair10"),multiarg=FALSE)
check.text.args("refdb",refdb,c("ucsc","refseq"))
check.text.args("what",what,c("queries","fields"))
switch(type,
gene = {
switch(refdb,
ucsc = {
switch(org,
hg18 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
hg19 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
hg38 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
mm9 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
mm10 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
rn5 = {
return(list(
mgcGenes=get.ucsc.tbl.tpl("mgcGenes",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm3 = {
return(list(
flyBaseCanonical=
get.ucsc.tbl.tpl("flyBaseCanonical",what),
flyBaseGene=
get.ucsc.tbl.tpl("flyBaseGene",what),
flyBaseToRefSeq=
get.ucsc.tbl.tpl("flyBaseToRefSeq",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm6 = {
# Stub until we find out what will happen with
# Augustus
},
danrer7 = {
return(list(
mgcGenes=get.ucsc.tbl.tpl("mgcGenes",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
pantro4 = {
warnwrap("No UCSC Genome annotation for Pan ",
"troglodytes! Will use RefSeq instead...",
now=TRUE)
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
susscr3 = {
warnwrap("No UCSC Genome annotation for Sus ",
"scrofa! Will use RefSeq instead...",
now=TRUE)
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Borwser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
},
refseq = {
switch(org,
hg18 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what)
))
},
hg19 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
hg38 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what)
))
},
mm9 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
mm10 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
rn5 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm3 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
pantro4 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
susscr3 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Borwser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
}
)
},
exon = {
switch(refdb,
ucsc = {
switch(org,
hg18 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
hg19 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
hg38 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
mm9 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
mm10 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
rn5 = {
return(list(
mgcGenes=get.ucsc.tbl.tpl("mgcGenes",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm3 = {
return(list(
flyBaseCanonical=
get.ucsc.tbl.tpl("flyBaseCanonical",what),
flyBaseGene=
get.ucsc.tbl.tpl("flyBaseGene",what),
flyBaseToRefSeq=
get.ucsc.tbl.tpl("flyBaseToRefSeq",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(list(
mgcGenes=get.ucsc.tbl.tpl("mgcGenes",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
pantro4 = {
warnwrap("No UCSC Genome annotation for Pan ",
"troglodytes! Will use RefSeq instead...",
now=TRUE)
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
susscr3 = {
warnwrap("No UCSC Genome annotation for Sus ",
"scrofa! Will use RefSeq instead...",
now=TRUE)
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Borwser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
},
refseq = {
switch(org,
hg18 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what)
))
},
hg19 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
hg38 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what)
))
},
mm9 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
mm10 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
rn5 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm3 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
pantro4 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
susscr3 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Borwser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
}
)
}
)
}
#' Create SQLite UCSC table template defintions
#'
#' Returns an SQLIte table template defintion, according to UCSC Genome Browser
#' database table schemas. This functionality is used when the package RMySQL
#' is not available for some reason, e.g. Windows machines. Internal use only.
#'
#' @param tab name of UCSC database table.
#' @param what \code{"queries"} for SQLite table definitions or \code{"fields"}
#' for table column names.
#' @return An SQLite table definition.
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.table.tmpl <- get.ucsc.tbl.tpl("knownCanonical")
#'}
get.ucsc.tbl.tpl <- function(tab,what="queries") {
if (what=="queries") {
switch(tab,
knownCanonical = {
return(paste(
"CREATE TABLE",
"`knownCanonical` (",
"`chrom` TEXT NOT NULL DEFAULT '',",
"`chromStart` INTEGER NOT NULL DEFAULT '0',",
"`chromEnd` INTEGER NOT NULL DEFAULT '0',",
"`clusterId` INTEGER NOT NULL DEFAULT '0',",
"`transcript` TEXT NOT NULL DEFAULT '',",
"`protein` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
knownGene = {
return(paste(
"CREATE TABLE",
"`knownGene` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`chrom` TEXT NOT NULL DEFAULT '',",
"`strand` TEXT NOT NULL DEFAULT '',",
"`txStart` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`txEnd` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`cdsStart` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`cdsEnd` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`exonCount` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`exonStarts` TEXT NOT NULL,",
"`exonEnds` TEXT NOT NULL,",
"`proteinID` TEXT NOT NULL DEFAULT '',",
"`alignID` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
knownToRefSeq = {
return(paste(
"CREATE TABLE",
"`knownToRefSeq` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`value` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
refFlat = {
return(paste("CREATE TABLE",
"`refFlat` (",
"`geneName` TEXT NOT NULL,",
"`name` TEXT NOT NULL,",
"`chrom` TEXT NOT NULL,",
"`strand` TEXT NOT NULL,",
"`txStart` UNSIGNED INTEGER NOT NULL,",
"`txEnd` UNSIGNED INTEGER NOT NULL,",
"`cdsStart` UNSIGNED INTEGER NOT NULL,",
"`cdsEnd` UNSIGNED INTEGER NOT NULL,",
"`exonCount` UNSIGNED INTEGER NOT NULL,",
"`exonStarts` TEXT NOT NULL,",
"`exonEnds` TEXT NOT NULL",
")",collapse=" "
))
},
knownToEnsembl = {
return(paste(
"CREATE TABLE",
"`knownToEnsembl` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`value` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
ensemblSource = {
return(paste(
"CREATE TABLE",
"`ensemblSource` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`source` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
mgcGenes = {
return(paste(
"CREATE TABLE `mgcGenes` (",
"`bin` UNSIGNED INTEGER NOT NULL,",
"`name` TEXT NOT NULL,",
"`chrom` TEXT NOT NULL,",
"`strand` TEXT NOT NULL,",
"`txStart` UNSIGNED INTEGER NOT NULL,",
"`txEnd` UNSIGNED INTEGER NOT NULL,",
"`cdsStart` UNSIGNED INTEGER NOT NULL,",
"`cdsEnd` UNSIGNED INTEGER NOT NULL,",
"`exonCount` UNSIGNED INTEGER NOT NULL,",
"`exonStarts` TEXT NOT NULL,",
"`exonEnds` TEXT NOT NULL,",
"`score` INTEGER DEFAULT NULL,",
"`name2` TEXT NOT NULL,",
"`cdsStartStat` TEXT NOT NULL,",
"`cdsEndStat` TEXT NOT NULL,",
"`exonFrames` TEXT NOT NULL",
")",collapse=" "
))
},
ensemblToGeneName = {
return(paste(
"CREATE TABLE",
"`knownToGeneName` (",
"`name` TEXT NOT NULL,",
"`value` TEXT NOT NULL",
")",collapse=" "
))
},
flyBaseCanonical = {
return(paste(
"CREATE TABLE",
"`flyBaseCanonical` (",
"`chrom` TEXT NOT NULL DEFAULT '',",
"`chromStart` INTEGER NOT NULL DEFAULT '0',",
"`chromEnd` INTEGER NOT NULL DEFAULT '0',",
"`clusterId` INTEGER unsigned NOT NULL DEFAULT '0',",
"`transcript` TEXT NOT NULL DEFAULT '',",
"`protein` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
flyBaseGene = {
return(paste(
"CREATE TABLE",
"`flyBaseGene` (",
"`bin` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`name` TEXT NOT NULL DEFAULT '',",
"`chrom` TEXT NOT NULL DEFAULT '',",
"`strand` TEXT NOT NULL DEFAULT '',",
"`txStart` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`txEnd` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`cdsStart` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`cdsEnd` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`exonCount` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`exonStarts` TEXT NOT NULL,",
"`exonEnds` TEXT NOT NULL",
")",collapse=" "
))
},
flyBaseToRefSeq = {
return(paste(
"CREATE TABLE",
"`flyBaseToRefSeq` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`value` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
}
)
}
else if (what=="fields") {
switch(tab,
knownCanonical = {
return(c("chrom","chromStart","chromEnd","clusterId",
"transcript","protein"))
},
knownGene = {
return(c("name","chrom","strand","txStart","txEnd","cdsStart",
"cdsEnd","exonCount","exonStarts","exonEnds","proteinID",
"alignID"))
},
knownToRefSeq = {
return(c("name","value"))
},
refFlat = {
return(c("geneName","name","chrom","strand","txStart","txEnd",
"cdsStart","cdsEnd","exonCount","exonStarts","exonEnds"))
},
knownToEnsembl = {
return(c("name","value"))
},
ensemblSource = {
return(c("name","source"))
},
mgcGenes = {
return(c("name","chrom","strand","txStart","txEnd","cdsStart",
"cdsEnd","exonCount","exonStarts","exonEnds","score",
"name2","cdsStartStat","cdsEndStat","exonFrames"
))
},
ensemblToGeneName = {
return(c("name","value"))
},
flyBaseCanonical = {
return(c("chrom","chromStart","chromEnd","clusterId",
"transcript","protein"))
},
flyBaseGene = {
return(c("bin","name","chrom","strand","txStart","txEnd",
"cdsStart","cdsEnd","exonCount","exonStarts","exonEnds"))
},
flyBaseToRefSeq = {
return(c("name","value"))
}
)
}
}
#' Return queries for the UCSC Genome Browser database, according to organism and
#' source
#'
#' Returns an SQL query to be used with a connection to the UCSC Genome Browser
#' database and fetch metaseqR supported organism annotations. This query is
#' constructed based on the data source and data type to be returned.
#'
#' @param org one of metaseqR supported organisms.
#' @param type either \code{"gene"} or \code{"exon"}.
#' @param refdb one of \code{"ucsc"} or \code{"refseq"} to use the UCSC or RefSeq
#' annotation sources respectively.
#' @return A valid SQL query.
#' @export
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.query <- get.ucsc.query("hg18","gene","ucsc")
#'}
get.ucsc.query <- function(org,type,refdb="ucsc") {
type <- tolower(type[1])
org <- tolower(org[1])
refdb <- tolower(refdb[1])
check.text.args("type",type,c("gene","exon"))
check.text.args("org",org,c("hg18","hg19","hg38","mm9","mm10","rn5","dm3",
"dm6","danrer7","pantro4","susscr3","tair10"),multiarg=FALSE)
check.text.args("refdb",refdb,c("ucsc","refseq"))
switch(type,
gene = {
switch(refdb,
ucsc = {
switch(org,
hg18 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,knownGene.strand ",
"AS `strand`,`geneName` AS `gene_name`,'NA' ",
"AS `biotype` FROM `knownCanonical` INNER ",
"JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
},
hg19 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,",
"knownGene.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownCanonical` INNER JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
},
hg38 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,knownGene.strand ",
"AS `strand`,`geneName` AS `gene_name`,'NA' ",
"AS `biotype` FROM `knownCanonical` INNER ",
"JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
# Should be the same as hg19 but is like hg18
},
mm9 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,",
"knownGene.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownCanonical` INNER JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
},
mm10 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,",
"knownGene.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownCanonical` INNER JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
},
rn5 = {
return(paste("SELECT mgcGenes.chrom AS ",
"`chromosome`,`txStart` AS `start`,`txEnd` ",
"AS `end`,mgcGenes.name AS `gene_id`,0 AS ",
"`gc_content`,mgcGenes.strand AS `strand`,",
"`name2` AS `gene_name`,`source` AS `biotype` ",
"FROM `mgcGenes` INNER JOIN ",
"`ensemblToGeneName` ON ",
"mgcGenes.name2=ensemblToGeneName.value INNER ",
"JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm3 = {
return(paste("SELECT flyBaseCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,",
"flyBaseGene.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`flyBaseCanonical` INNER JOIN `flyBaseGene` ",
"ON flyBaseCanonical.transcript=",
"flyBaseGene.name INNER JOIN ",
"`flyBaseToRefSeq` ON ",
"flyBaseCanonical.transcript=",
"flyBaseToRefSeq.name INNER JOIN `refFlat` ON ",
"flyBaseToRefSeq.value=refFlat.name INNER ",
"JOIN `ensemblToGeneName` ON ",
"ensemblToGeneName.value=refFlat.geneName ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(paste("SELECT mgcGenes.chrom AS ",
"`chromosome`,`txStart` AS `start`,`txEnd` ",
"AS `end`,mgcGenes.name AS `gene_id`,0 AS ",
"`gc_content`,mgcGenes.strand AS `strand`,",
"`name2` AS `gene_name`,`source` AS `biotype` ",
"FROM `mgcGenes` INNER JOIN ",
"`ensemblToGeneName` ON ",
"mgcGenes.name2=ensemblToGeneName.value INNER ",
"JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
pantro4 = {
warnwrap("No UCSC Genome annotation for Pan ",
"troglodytes! Will use RefSeq instead...",
now=TRUE)
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
susscr3 = {
warnwrap("No UCSC Genome annotation for Sus ",
"scrofa! Will use RefSeq instead...",
now=TRUE)
return(paste(
"SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`, refFlat.txEnd AS ",
"`end`, refFlat.name AS `gene_id`, 0 AS ",
"`gc_content`, refFlat.strand AS `strand`,",
"`geneName` AS `gene_name`, `source` AS ",
"`biotype` FROM `refFlat` INNER JOIN ",
"`ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`,",
"`start`",
sep=""
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Browser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
},
refseq = {
switch(org,
hg18 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,refFlat.strand ",
"AS `strand`,`geneName` AS `gene_name`,'NA' ",
"AS `biotype` FROM `refFlat` INNER JOIN ",
"`knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
},
hg19 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER ",
"JOIN `knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
},
hg38 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,refFlat.strand ",
"AS `strand`,`geneName` AS `gene_name`,'NA' ",
"AS `biotype` FROM `refFlat` INNER JOIN ",
"`knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
# Should be the same as hg19 but is as hg18
},
mm9 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER ",
"JOIN `knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
},
mm10 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER ",
"JOIN `knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
},
rn5 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm3 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,refFlat.strand ",
"AS `strand`,`geneName` AS `gene_name`,",
"`source` AS `biotype` FROM `refFlat` INNER ",
"JOIN `ensemblToGeneName` ON ",
"ensemblToGeneName.value=refFlat.geneName ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
pantro4 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
susscr3 = {
return(paste(
"SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`, refFlat.txEnd AS ",
"`end`, refFlat.name AS `gene_id`, 0 AS ",
"`gc_content`, refFlat.strand AS `strand`,",
"`geneName` AS `gene_name`, `source` AS ",
"`biotype` FROM `refFlat` INNER JOIN ",
"`ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`,",
"`start`",
sep=""
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Browser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
}
)
},
exon = {
switch(refdb,
ucsc = {
switch(org,
hg18 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,'NA' AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
},
hg19 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
},
hg38 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,'NA' AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
# Should be the same as hg19 but is as hg18
},
mm9 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
},
mm10 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
},
rn5 = {
return(paste("SELECT mgcGenes.chrom AS ",
"`chromosome`,`exonStarts` AS `start`,",
"`exonEnds` AS `end`,mgcGenes.name AS ",
"`exon_id`,mgcGenes.strand AS `strand`,",
"mgcGenes.name AS `gene_id`,`name2` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`mgcGenes` INNER JOIN `ensemblToGeneName` ON ",
"mgcGenes.name2=ensemblToGeneName.value INNER ",
"JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm3 = {
return(paste("SELECT flyBaseCanonical.chrom AS ",
"`chromosome`,flyBaseGene.exonStarts AS ",
"`start`,flyBaseGene.exonEnds AS `end`,",
"`transcript` AS `exon_id`,flyBaseGene.strand ",
"AS `strand`,`transcript` AS `gene_id`,",
"`geneName` AS `gene_name`,`source` AS ",
"`biotype` FROM `flyBaseCanonical` INNER JOIN ",
"`flyBaseGene` ON ",
"flyBaseCanonical.transcript=flyBaseGene.name ",
"INNER JOIN `flyBaseToRefSeq` ON ",
"flyBaseCanonical.transcript=",
"flyBaseToRefSeq.name INNER JOIN `refFlat` ON ",
"flyBaseToRefSeq.value=refFlat.name ",
"INNER JOIN `ensemblToGeneName` ON ",
"ensemblToGeneName.value=refFlat.geneName ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(paste("SELECT mgcGenes.chrom AS ",
"`chromosome`,`exonStarts` AS `start`,",
"`exonEnds` AS `end`,mgcGenes.name AS ",
"`exon_id`,mgcGenes.strand AS `strand`,",
"mgcGenes.name AS `gene_id`,`name2` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`mgcGenes` INNER JOIN `ensemblToGeneName` ON ",
"mgcGenes.name2=ensemblToGeneName.value INNER ",
"JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
pantro4 = {
warnwrap("No UCSC Genome annotation for Pan ",
"troglodytes! Will use RefSeq instead...",
now=TRUE)
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
susscr3 = {
warnwrap("No UCSC Genome annotation for Sus ",
"scrofa! Will use RefSeq instead...",
now=TRUE)
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Browser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
},
refseq = {
switch(org,
hg18 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,'NA' AS `biotype` FROM `refFlat` ",
"INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
hg19 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
hg38 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,'NA' AS `biotype` FROM `refFlat` ",
"INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
# Should be the same as hg19 but is as hg18
},
mm9 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
mm10 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
rn5 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm3 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"ensemblToGeneName.value=refFlat.geneName ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
pantro4 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
susscr3 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Browser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
}
)
}
)
}
#' Return host, username and password for UCSC Genome Browser database
#'
#' Returns a character vector with a hostname, username and password to connect
#' to the UCSC Genome Browser database to retrieve annotation. Internal use.
#'
#' @return A named character vector.
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.creds <- get.ucsc.credentials()
#'}
get.ucsc.credentials <- function() {
return(c(
host="genome-mysql.cse.ucsc.edu",
user="genome",
password=""
))
}
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R Package Documentation
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Defines functions get.ucsc.credentials get.ucsc.query get.ucsc.tbl.tpl get.ucsc.tabledef get.ucsc.dbl
Documented in get.ucsc.credentials get.ucsc.dbl get.ucsc.query get.ucsc.tabledef get.ucsc.tbl.tpl
#' Download annotation from UCSC servers, according to organism and source
#'
#' Directly downloads UCSC and RefSeq annotation files from UCSC servers to be
#' used with metaseqR. This functionality is used when the package RMySQL is not
#' available for some reason, e.g. Windows machines.
#'
#' @param org one of metaseqR supported organisms.
#' @param type either \code{"gene"} or \code{"exon"}.
#' @param refdb one of \code{"ucsc"} or \code{"refseq"} to use the UCSC or RefSeq
#' annotation sources respectively.
#' @return A data frame with annotation elements.
#' @export
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.file <- get.ucsc.file("hg18","gene","ucsc")
#'}
get.ucsc.dbl <- function(org,type,refdb="ucsc") {
type <- tolower(type[1])
org <- tolower(org[1])
refdb <- tolower(refdb[1])
check.text.args("type",type,c("gene","exon"))
check.text.args("org",org,c("hg18","hg19","hg38","mm9","mm10","rn5","dm3",
"dm6","danrer7","pantro4","susscr3","tair10"),multiarg=FALSE)
check.text.args("refdb",refdb,c("ucsc","refseq"))
if (!require(RSQLite))
stopwrap("R package RSQLite is required to use annotation from UCSC!")
http.base <- paste("http://hgdownload.soe.ucsc.edu/goldenPath/",
get.ucsc.organism(org),"/database/",sep="")
table.defs <- get.ucsc.tabledef(org,type,refdb,"fields")
file.list <- vector("list",length(table.defs))
names(file.list) <- names(table.defs)
for (n in names(file.list))
file.list[[n]] <- paste(http.base,n,".txt.gz",sep="")
# Fill the fields for each table
drv <- dbDriver("SQLite")
db.tmp <- tempfile()
con <- dbConnect(drv,dbname=db.tmp)
#disp(" Defining tables for temporary SQLite ",refdb," ",org," ",
# type," subset database")
#for (n in names(file.list)) {
# disp(" Creating table ",n,"\n")
# dbSendQuery(con,table.defs[[n]])
#}
disp(" Retrieving tables for temporary SQLite ",refdb," ",org," ",type,
" subset database")
for (n in names(file.list)) {
disp(" Retrieving table ",n)
download.file(file.list[[n]],file.path(tempdir(),
paste(n,".txt.gz",sep="")),quiet=TRUE)
if (.Platform$OS.type == "unix")
system(paste("gzip -df",file.path(tempdir(),
paste(n,".txt.gz",sep=""))))
else
unzip(file.path(tempdir(),paste(n,".txt.gz",sep="")))
sql.df <- read.delim(file.path(tempdir(),paste(n,".txt",sep="")),
row.names=NULL,header=FALSE,strip.white=TRUE)
names(sql.df) <- table.defs[[n]]
dbWriteTable(con,n,sql.df,row.names=FALSE)
}
dbDisconnect(con)
return(db.tmp)
}
#' Get SQLite UCSC table defintions, according to organism and source
#'
#' Creates a list of UCSC Genome Browser database tables and their SQLite
#' definitions with the purpose of creating a temporary SQLite database to be
#' used used with metaseqR. This functionality is used when the package RMySQL
#' is not available for some reason, e.g. Windows machines.
#'
#' @param org one of metaseqR supported organisms.
#' @param type either \code{"gene"} or \code{"exon"}.
#' @param refdb one of \code{"ucsc"} or \code{"refseq"} to use the UCSC or RefSeq
#' annotation sources respectively.
#' @return A list with SQLite table definitions.
#' @export
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.tabledefs <- get.ucsc.tables("hg18","gene","ucsc")
#'}
get.ucsc.tabledef <- function(org,type,refdb="ucsc",what="queries") {
type <- tolower(type[1])
org <- tolower(org[1])
refdb <- tolower(refdb[1])
what <- tolower(what[1])
check.text.args("type",type,c("gene","exon"))
check.text.args("org",org,c("hg18","hg19","hg38","mm9","mm10","rn5","dm3",
"dm6","danrer7","pantro4","susscr3","tair10"),multiarg=FALSE)
check.text.args("refdb",refdb,c("ucsc","refseq"))
check.text.args("what",what,c("queries","fields"))
switch(type,
gene = {
switch(refdb,
ucsc = {
switch(org,
hg18 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
hg19 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
hg38 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
mm9 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
mm10 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
rn5 = {
return(list(
mgcGenes=get.ucsc.tbl.tpl("mgcGenes",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm3 = {
return(list(
flyBaseCanonical=
get.ucsc.tbl.tpl("flyBaseCanonical",what),
flyBaseGene=
get.ucsc.tbl.tpl("flyBaseGene",what),
flyBaseToRefSeq=
get.ucsc.tbl.tpl("flyBaseToRefSeq",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm6 = {
# Stub until we find out what will happen with
# Augustus
},
danrer7 = {
return(list(
mgcGenes=get.ucsc.tbl.tpl("mgcGenes",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
pantro4 = {
warnwrap("No UCSC Genome annotation for Pan ",
"troglodytes! Will use RefSeq instead...",
now=TRUE)
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
susscr3 = {
warnwrap("No UCSC Genome annotation for Sus ",
"scrofa! Will use RefSeq instead...",
now=TRUE)
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Borwser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
},
refseq = {
switch(org,
hg18 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what)
))
},
hg19 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
hg38 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what)
))
},
mm9 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
mm10 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
rn5 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm3 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
pantro4 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
susscr3 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Borwser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
}
)
},
exon = {
switch(refdb,
ucsc = {
switch(org,
hg18 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
hg19 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
hg38 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
mm9 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
mm10 = {
return(list(
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownGene=get.ucsc.tbl.tpl("knownGene",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what),
refFlat=get.ucsc.tbl.tpl("refFlat",what)
))
},
rn5 = {
return(list(
mgcGenes=get.ucsc.tbl.tpl("mgcGenes",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm3 = {
return(list(
flyBaseCanonical=
get.ucsc.tbl.tpl("flyBaseCanonical",what),
flyBaseGene=
get.ucsc.tbl.tpl("flyBaseGene",what),
flyBaseToRefSeq=
get.ucsc.tbl.tpl("flyBaseToRefSeq",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(list(
mgcGenes=get.ucsc.tbl.tpl("mgcGenes",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
pantro4 = {
warnwrap("No UCSC Genome annotation for Pan ",
"troglodytes! Will use RefSeq instead...",
now=TRUE)
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
susscr3 = {
warnwrap("No UCSC Genome annotation for Sus ",
"scrofa! Will use RefSeq instead...",
now=TRUE)
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Borwser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
},
refseq = {
switch(org,
hg18 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what)
))
},
hg19 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
hg38 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what)
))
},
mm9 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
mm10 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
knownToRefSeq=
get.ucsc.tbl.tpl("knownToRefSeq",what),
knownCanonical=
get.ucsc.tbl.tpl("knownCanonical",what),
knownToEnsembl=
get.ucsc.tbl.tpl("knownToEnsembl",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
rn5 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm3 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
pantro4 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
susscr3 = {
return(list(
refFlat=get.ucsc.tbl.tpl("refFlat",what),
ensemblToGeneName=
get.ucsc.tbl.tpl("ensemblToGeneName",what),
ensemblSource=
get.ucsc.tbl.tpl("ensemblSource",what)
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Borwser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
}
)
}
)
}
#' Create SQLite UCSC table template defintions
#'
#' Returns an SQLIte table template defintion, according to UCSC Genome Browser
#' database table schemas. This functionality is used when the package RMySQL
#' is not available for some reason, e.g. Windows machines. Internal use only.
#'
#' @param tab name of UCSC database table.
#' @param what \code{"queries"} for SQLite table definitions or \code{"fields"}
#' for table column names.
#' @return An SQLite table definition.
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.table.tmpl <- get.ucsc.tbl.tpl("knownCanonical")
#'}
get.ucsc.tbl.tpl <- function(tab,what="queries") {
if (what=="queries") {
switch(tab,
knownCanonical = {
return(paste(
"CREATE TABLE",
"`knownCanonical` (",
"`chrom` TEXT NOT NULL DEFAULT '',",
"`chromStart` INTEGER NOT NULL DEFAULT '0',",
"`chromEnd` INTEGER NOT NULL DEFAULT '0',",
"`clusterId` INTEGER NOT NULL DEFAULT '0',",
"`transcript` TEXT NOT NULL DEFAULT '',",
"`protein` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
knownGene = {
return(paste(
"CREATE TABLE",
"`knownGene` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`chrom` TEXT NOT NULL DEFAULT '',",
"`strand` TEXT NOT NULL DEFAULT '',",
"`txStart` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`txEnd` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`cdsStart` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`cdsEnd` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`exonCount` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`exonStarts` TEXT NOT NULL,",
"`exonEnds` TEXT NOT NULL,",
"`proteinID` TEXT NOT NULL DEFAULT '',",
"`alignID` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
knownToRefSeq = {
return(paste(
"CREATE TABLE",
"`knownToRefSeq` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`value` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
refFlat = {
return(paste("CREATE TABLE",
"`refFlat` (",
"`geneName` TEXT NOT NULL,",
"`name` TEXT NOT NULL,",
"`chrom` TEXT NOT NULL,",
"`strand` TEXT NOT NULL,",
"`txStart` UNSIGNED INTEGER NOT NULL,",
"`txEnd` UNSIGNED INTEGER NOT NULL,",
"`cdsStart` UNSIGNED INTEGER NOT NULL,",
"`cdsEnd` UNSIGNED INTEGER NOT NULL,",
"`exonCount` UNSIGNED INTEGER NOT NULL,",
"`exonStarts` TEXT NOT NULL,",
"`exonEnds` TEXT NOT NULL",
")",collapse=" "
))
},
knownToEnsembl = {
return(paste(
"CREATE TABLE",
"`knownToEnsembl` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`value` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
ensemblSource = {
return(paste(
"CREATE TABLE",
"`ensemblSource` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`source` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
mgcGenes = {
return(paste(
"CREATE TABLE `mgcGenes` (",
"`bin` UNSIGNED INTEGER NOT NULL,",
"`name` TEXT NOT NULL,",
"`chrom` TEXT NOT NULL,",
"`strand` TEXT NOT NULL,",
"`txStart` UNSIGNED INTEGER NOT NULL,",
"`txEnd` UNSIGNED INTEGER NOT NULL,",
"`cdsStart` UNSIGNED INTEGER NOT NULL,",
"`cdsEnd` UNSIGNED INTEGER NOT NULL,",
"`exonCount` UNSIGNED INTEGER NOT NULL,",
"`exonStarts` TEXT NOT NULL,",
"`exonEnds` TEXT NOT NULL,",
"`score` INTEGER DEFAULT NULL,",
"`name2` TEXT NOT NULL,",
"`cdsStartStat` TEXT NOT NULL,",
"`cdsEndStat` TEXT NOT NULL,",
"`exonFrames` TEXT NOT NULL",
")",collapse=" "
))
},
ensemblToGeneName = {
return(paste(
"CREATE TABLE",
"`knownToGeneName` (",
"`name` TEXT NOT NULL,",
"`value` TEXT NOT NULL",
")",collapse=" "
))
},
flyBaseCanonical = {
return(paste(
"CREATE TABLE",
"`flyBaseCanonical` (",
"`chrom` TEXT NOT NULL DEFAULT '',",
"`chromStart` INTEGER NOT NULL DEFAULT '0',",
"`chromEnd` INTEGER NOT NULL DEFAULT '0',",
"`clusterId` INTEGER unsigned NOT NULL DEFAULT '0',",
"`transcript` TEXT NOT NULL DEFAULT '',",
"`protein` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
},
flyBaseGene = {
return(paste(
"CREATE TABLE",
"`flyBaseGene` (",
"`bin` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`name` TEXT NOT NULL DEFAULT '',",
"`chrom` TEXT NOT NULL DEFAULT '',",
"`strand` TEXT NOT NULL DEFAULT '',",
"`txStart` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`txEnd` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`cdsStart` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`cdsEnd` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`exonCount` UNSIGNED INTEGER NOT NULL DEFAULT '0',",
"`exonStarts` TEXT NOT NULL,",
"`exonEnds` TEXT NOT NULL",
")",collapse=" "
))
},
flyBaseToRefSeq = {
return(paste(
"CREATE TABLE",
"`flyBaseToRefSeq` (",
"`name` TEXT NOT NULL DEFAULT '',",
"`value` TEXT NOT NULL DEFAULT ''",
")",collapse=" "
))
}
)
}
else if (what=="fields") {
switch(tab,
knownCanonical = {
return(c("chrom","chromStart","chromEnd","clusterId",
"transcript","protein"))
},
knownGene = {
return(c("name","chrom","strand","txStart","txEnd","cdsStart",
"cdsEnd","exonCount","exonStarts","exonEnds","proteinID",
"alignID"))
},
knownToRefSeq = {
return(c("name","value"))
},
refFlat = {
return(c("geneName","name","chrom","strand","txStart","txEnd",
"cdsStart","cdsEnd","exonCount","exonStarts","exonEnds"))
},
knownToEnsembl = {
return(c("name","value"))
},
ensemblSource = {
return(c("name","source"))
},
mgcGenes = {
return(c("name","chrom","strand","txStart","txEnd","cdsStart",
"cdsEnd","exonCount","exonStarts","exonEnds","score",
"name2","cdsStartStat","cdsEndStat","exonFrames"
))
},
ensemblToGeneName = {
return(c("name","value"))
},
flyBaseCanonical = {
return(c("chrom","chromStart","chromEnd","clusterId",
"transcript","protein"))
},
flyBaseGene = {
return(c("bin","name","chrom","strand","txStart","txEnd",
"cdsStart","cdsEnd","exonCount","exonStarts","exonEnds"))
},
flyBaseToRefSeq = {
return(c("name","value"))
}
)
}
}
#' Return queries for the UCSC Genome Browser database, according to organism and
#' source
#'
#' Returns an SQL query to be used with a connection to the UCSC Genome Browser
#' database and fetch metaseqR supported organism annotations. This query is
#' constructed based on the data source and data type to be returned.
#'
#' @param org one of metaseqR supported organisms.
#' @param type either \code{"gene"} or \code{"exon"}.
#' @param refdb one of \code{"ucsc"} or \code{"refseq"} to use the UCSC or RefSeq
#' annotation sources respectively.
#' @return A valid SQL query.
#' @export
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.query <- get.ucsc.query("hg18","gene","ucsc")
#'}
get.ucsc.query <- function(org,type,refdb="ucsc") {
type <- tolower(type[1])
org <- tolower(org[1])
refdb <- tolower(refdb[1])
check.text.args("type",type,c("gene","exon"))
check.text.args("org",org,c("hg18","hg19","hg38","mm9","mm10","rn5","dm3",
"dm6","danrer7","pantro4","susscr3","tair10"),multiarg=FALSE)
check.text.args("refdb",refdb,c("ucsc","refseq"))
switch(type,
gene = {
switch(refdb,
ucsc = {
switch(org,
hg18 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,knownGene.strand ",
"AS `strand`,`geneName` AS `gene_name`,'NA' ",
"AS `biotype` FROM `knownCanonical` INNER ",
"JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
},
hg19 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,",
"knownGene.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownCanonical` INNER JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
},
hg38 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,knownGene.strand ",
"AS `strand`,`geneName` AS `gene_name`,'NA' ",
"AS `biotype` FROM `knownCanonical` INNER ",
"JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
# Should be the same as hg19 but is like hg18
},
mm9 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,",
"knownGene.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownCanonical` INNER JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
},
mm10 = {
return(paste("SELECT knownCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,",
"knownGene.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownCanonical` INNER JOIN `knownGene` ON ",
"knownCanonical.transcript=knownGene.name ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"`gene_id` ORDER BY `chromosome`, `start`",
sep=""))
},
rn5 = {
return(paste("SELECT mgcGenes.chrom AS ",
"`chromosome`,`txStart` AS `start`,`txEnd` ",
"AS `end`,mgcGenes.name AS `gene_id`,0 AS ",
"`gc_content`,mgcGenes.strand AS `strand`,",
"`name2` AS `gene_name`,`source` AS `biotype` ",
"FROM `mgcGenes` INNER JOIN ",
"`ensemblToGeneName` ON ",
"mgcGenes.name2=ensemblToGeneName.value INNER ",
"JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm3 = {
return(paste("SELECT flyBaseCanonical.chrom AS ",
"`chromosome`,`chromStart` AS `start`,",
"`chromEnd` AS `end`,`transcript` AS ",
"`gene_id`,0 AS `gc_content`,",
"flyBaseGene.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`flyBaseCanonical` INNER JOIN `flyBaseGene` ",
"ON flyBaseCanonical.transcript=",
"flyBaseGene.name INNER JOIN ",
"`flyBaseToRefSeq` ON ",
"flyBaseCanonical.transcript=",
"flyBaseToRefSeq.name INNER JOIN `refFlat` ON ",
"flyBaseToRefSeq.value=refFlat.name INNER ",
"JOIN `ensemblToGeneName` ON ",
"ensemblToGeneName.value=refFlat.geneName ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(paste("SELECT mgcGenes.chrom AS ",
"`chromosome`,`txStart` AS `start`,`txEnd` ",
"AS `end`,mgcGenes.name AS `gene_id`,0 AS ",
"`gc_content`,mgcGenes.strand AS `strand`,",
"`name2` AS `gene_name`,`source` AS `biotype` ",
"FROM `mgcGenes` INNER JOIN ",
"`ensemblToGeneName` ON ",
"mgcGenes.name2=ensemblToGeneName.value INNER ",
"JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
pantro4 = {
warnwrap("No UCSC Genome annotation for Pan ",
"troglodytes! Will use RefSeq instead...",
now=TRUE)
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
susscr3 = {
warnwrap("No UCSC Genome annotation for Sus ",
"scrofa! Will use RefSeq instead...",
now=TRUE)
return(paste(
"SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`, refFlat.txEnd AS ",
"`end`, refFlat.name AS `gene_id`, 0 AS ",
"`gc_content`, refFlat.strand AS `strand`,",
"`geneName` AS `gene_name`, `source` AS ",
"`biotype` FROM `refFlat` INNER JOIN ",
"`ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`,",
"`start`",
sep=""
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Browser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
},
refseq = {
switch(org,
hg18 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,refFlat.strand ",
"AS `strand`,`geneName` AS `gene_name`,'NA' ",
"AS `biotype` FROM `refFlat` INNER JOIN ",
"`knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
},
hg19 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER ",
"JOIN `knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
},
hg38 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,refFlat.strand ",
"AS `strand`,`geneName` AS `gene_name`,'NA' ",
"AS `biotype` FROM `refFlat` INNER JOIN ",
"`knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
# Should be the same as hg19 but is as hg18
},
mm9 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER ",
"JOIN `knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
},
mm10 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER ",
"JOIN `knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY refFlat.name ORDER BY `chromosome`,",
" `start`",
sep=""))
},
rn5 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm3 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,refFlat.strand ",
"AS `strand`,`geneName` AS `gene_name`,",
"`source` AS `biotype` FROM `refFlat` INNER ",
"JOIN `ensemblToGeneName` ON ",
"ensemblToGeneName.value=refFlat.geneName ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
pantro4 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,refFlat.name AS ",
"`gene_id`,0 AS `gc_content`,",
"refFlat.strand AS `strand`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
susscr3 = {
return(paste(
"SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`, refFlat.txEnd AS ",
"`end`, refFlat.name AS `gene_id`, 0 AS ",
"`gc_content`, refFlat.strand AS `strand`,",
"`geneName` AS `gene_name`, `source` AS ",
"`biotype` FROM `refFlat` INNER JOIN ",
"`ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`,",
"`start`",
sep=""
))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Browser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
}
)
},
exon = {
switch(refdb,
ucsc = {
switch(org,
hg18 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,'NA' AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
},
hg19 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
},
hg38 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,'NA' AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
# Should be the same as hg19 but is as hg18
},
mm9 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
},
mm10 = {
return(paste("SELECT knownGene.chrom AS ",
"`chromosome`,knownGene.exonStarts AS `start`,",
"knownGene.exonEnds AS `end`,knownGene.name ",
"AS `exon_id`,knownGene.strand AS `strand`,",
"`transcript` AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`knownGene` INNER JOIN `knownCanonical` ON ",
"knownGene.name=knownCanonical.transcript ",
"INNER JOIN `knownToRefSeq` ON ",
"knownCanonical.transcript=knownToRefSeq.name ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"INNER JOIN `refFlat` ON ",
"knownToRefSeq.value=refFlat.name GROUP BY ",
"knownGene.name ORDER BY `chromosome`, `start`",
sep=""))
},
rn5 = {
return(paste("SELECT mgcGenes.chrom AS ",
"`chromosome`,`exonStarts` AS `start`,",
"`exonEnds` AS `end`,mgcGenes.name AS ",
"`exon_id`,mgcGenes.strand AS `strand`,",
"mgcGenes.name AS `gene_id`,`name2` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`mgcGenes` INNER JOIN `ensemblToGeneName` ON ",
"mgcGenes.name2=ensemblToGeneName.value INNER ",
"JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm3 = {
return(paste("SELECT flyBaseCanonical.chrom AS ",
"`chromosome`,flyBaseGene.exonStarts AS ",
"`start`,flyBaseGene.exonEnds AS `end`,",
"`transcript` AS `exon_id`,flyBaseGene.strand ",
"AS `strand`,`transcript` AS `gene_id`,",
"`geneName` AS `gene_name`,`source` AS ",
"`biotype` FROM `flyBaseCanonical` INNER JOIN ",
"`flyBaseGene` ON ",
"flyBaseCanonical.transcript=flyBaseGene.name ",
"INNER JOIN `flyBaseToRefSeq` ON ",
"flyBaseCanonical.transcript=",
"flyBaseToRefSeq.name INNER JOIN `refFlat` ON ",
"flyBaseToRefSeq.value=refFlat.name ",
"INNER JOIN `ensemblToGeneName` ON ",
"ensemblToGeneName.value=refFlat.geneName ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(paste("SELECT mgcGenes.chrom AS ",
"`chromosome`,`exonStarts` AS `start`,",
"`exonEnds` AS `end`,mgcGenes.name AS ",
"`exon_id`,mgcGenes.strand AS `strand`,",
"mgcGenes.name AS `gene_id`,`name2` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`mgcGenes` INNER JOIN `ensemblToGeneName` ON ",
"mgcGenes.name2=ensemblToGeneName.value INNER ",
"JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
pantro4 = {
warnwrap("No UCSC Genome annotation for Pan ",
"troglodytes! Will use RefSeq instead...",
now=TRUE)
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
susscr3 = {
warnwrap("No UCSC Genome annotation for Sus ",
"scrofa! Will use RefSeq instead...",
now=TRUE)
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Browser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
},
refseq = {
switch(org,
hg18 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,'NA' AS `biotype` FROM `refFlat` ",
"INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
hg19 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
hg38 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,'NA' AS `biotype` FROM `refFlat` ",
"INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
# Should be the same as hg19 but is as hg18
},
mm9 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
mm10 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `knownToRefSeq` ON ",
"refFlat.name=knownToRefSeq.value INNER JOIN ",
"`knownCanonical` ON ",
"knownToRefSeq.name=knownCanonical.transcript ",
"INNER JOIN `knownToEnsembl` ON ",
"knownCanonical.transcript=knownToEnsembl.name",
" INNER JOIN `ensemblSource` ON ",
"knownToEnsembl.value=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
rn5 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm3 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"ensemblToGeneName.value=refFlat.geneName ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `gene_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
dm6 = {
# Stub until we find out what is going on with
# Augustus
},
danrer7 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
pantro4 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
susscr3 = {
return(paste("SELECT refFlat.chrom AS ",
"`chromosome`,refFlat.exonStarts AS `start`,",
"refFlat.exonEnds AS `end`,refFlat.name AS ",
"`exon_id`,refFlat.strand AS `strand`,",
"refFlat.name AS `gene_id`,`geneName` AS ",
"`gene_name`,`source` AS `biotype` FROM ",
"`refFlat` INNER JOIN `ensemblToGeneName` ON ",
"refFlat.geneName=ensemblToGeneName.value ",
"INNER JOIN `ensemblSource` ON ",
"ensemblToGeneName.name=ensemblSource.name ",
"GROUP BY `exon_id` ORDER BY `chromosome`, ",
"`start`",
sep=""))
},
tair10 = {
warnwrap("Arabidopsis thaliana genome is not ",
"supported by UCSC Genome Browser database! ",
"Will automatically switch to Ensembl...",
now=TRUE)
return(FALSE)
}
)
}
)
}
)
}
#' Return host, username and password for UCSC Genome Browser database
#'
#' Returns a character vector with a hostname, username and password to connect
#' to the UCSC Genome Browser database to retrieve annotation. Internal use.
#'
#' @return A named character vector.
#' @author Panagiotis Moulos
#' @examples
#' \dontrun{
#' db.creds <- get.ucsc.credentials()
#'}
get.ucsc.credentials <- function() {
return(c(
host="genome-mysql.cse.ucsc.edu",
user="genome",
password=""
))
}
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