R/metaseqr.query.R
In pmoulos/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=""
))
}
pmoulos/metaseqr documentation built on Dec. 29, 2020, 5:56 a.m.
R Package Documentation
Browse R Packages
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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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