R/query-ncbi.R
In pmoulos/sitadela: An R package for the easy provision of simple but complete tab-delimited genomic annotation from a variety of sources and organisms
Defines functions
.getUcscQueryNcbiExon
.getUcscQueryNcbiTranscript
.getUcscQueryNcbiGene
.getUcscTabledefNcbi
.getUcscTabledefNcbi <- function(org,what="queries") {
switch(org,
hg18 = {
warning("No NCBI RefSeq Genome annotation for Homo ",
"sapiens hg18! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
knownToRefSeq=
.getUcscTblTpl("knownToRefSeq",what),
knownCanonical=
.getUcscTblTpl("knownCanonical",what)
))
},
hg19 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
hg38 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
mm9 = {
warning("No NCBI RefSeq Genome annotation for Mus ",
"musculus mm9! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
knownToRefSeq=
.getUcscTblTpl("knownToRefSeq",what),
knownCanonical=
.getUcscTblTpl("knownCanonical",what),
knownToEnsembl=
.getUcscTblTpl("knownToEnsembl",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
mm10 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
rn5 = {
warning("No NCBI RefSeq Genome annotation for Rattus ",
"norvegicus rn5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
rn6 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
dm3 = {
warning("No NCBI RefSeq Genome annotation for Drosophila ",
"melanogaster dm3! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
dm6 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
danrer7 = {
warning("No NCBI RefSeq Genome annotation for Danio ",
"rerio danrer7! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
danrer10 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
danrer11 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
pantro4 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro4! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
pantro5 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
pantro6 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
susscr3 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v3! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
susscr11 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v11! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
equcab2 = {
warning("No NCBI RefSeq Genome annotation for Equus cabalus v2! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
equcab3 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
}
)
}
.getUcscQueryNcbiGene <- function(org) {
switch(org,
hg18 = {
warning("No NCBI RefSeq Genome annotation for Homo ",
"sapiens hg18! Will use UCSC RefSeq instead...",
immediate.=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`,",
"'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`"))
},
hg19 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
hg38 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
mm9 = {
warning("No NCBI RefSeq Genome annotation for Mus ",
"musculus mm9! Will use UCSC RefSeq instead...",
immediate.=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 `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`"))
},
mm10 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
rn5 = {
warning("No NCBI RefSeq Genome annotation for Rattus ",
"norvegicus rn5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
rn6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
dm3 = {
warning("No NCBI RefSeq Genome annotation for Drosophila ",
"melanogaster dm3! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
dm6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
danrer7 = {
warning("No NCBI RefSeq Genome annotation for Danio ",
"rerio danrer7! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
danrer10 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
danrer11 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
pantro4 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro4! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
pantro5 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
pantro6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
susscr3 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v3! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
susscr11 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v11! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
equcab2 = {
warning("No NCBI RefSeq Genome annotation for Equus cabalus v2! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
equcab3 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
}
)
}
.getUcscQueryNcbiTranscript <- function(org) {
switch(org,
hg18 = {
warning("No NCBI RefSeq Genome annotation for Homo ",
"sapiens hg18! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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",
"ORDER BY `chromosome`, `start`"))
},
hg19 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
hg38 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
mm9 = {
warning("No NCBI RefSeq Genome annotation for Mus ",
"musculus mm9! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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",
"ORDER BY `chromosome`,`start`"))
},
mm10 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
rn5 = {
warning("No NCBI RefSeq Genome annotation for Rattus ",
"norvegicus rn5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
rn6 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
dm3 = {
warning("No NCBI RefSeq Genome annotation for Drosophila ",
"melanogaster dm3! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
dm6 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
danrer7 = {
warning("No NCBI RefSeq Genome annotation for Danio ",
"rerio danrer7! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
danrer10 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
danrer11 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
pantro4 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro4! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
pantro5 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
pantro6 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
susscr3 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v3! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
susscr11 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v11! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
equcab2 = {
warning("No NCBI RefSeq Genome annotation for Equus cabalus v2! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
equcab3 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
}
)
}
.getUcscQueryNcbiExon <- function(org) {
switch(org,
hg18 = {
warning("No NCBI RefSeq Genome annotation for Homo ",
"sapiens hg18! Will use UCSC RefSeq instead...",
immediate.=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`,",
"'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`"))
},
hg19 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
hg38 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
mm9 = {
warning("No NCBI RefSeq Genome annotation for Mus ",
"musculus mm9! Will use UCSC RefSeq instead...",
immediate.=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 `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`"))
},
mm10 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
rn5 = {
warning("No NCBI RefSeq Genome annotation for Rattus ",
"norvegicus rn5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
rn6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
dm3 = {
warning("No NCBI RefSeq Genome annotation for Drosophila ",
"melanogaster dm3! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
dm6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
danrer7 = {
warning("No NCBI RefSeq Genome annotation for Danio ",
"rerio danrer7! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
danrer10 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
danrer11 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
pantro4 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro4! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
pantro5 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
pantro6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
susscr3 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v3! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
susscr11 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v11! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
equcab2 = {
warning("No NCBI RefSeq Genome annotation for Equus cabalus v2! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
equcab3 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
}
)
}
pmoulos/sitadela documentation built on May 19, 2024, 3:52 a.m.
R Package Documentation
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Defines functions .getUcscQueryNcbiExon .getUcscQueryNcbiTranscript .getUcscQueryNcbiGene .getUcscTabledefNcbi
.getUcscTabledefNcbi <- function(org,what="queries") {
switch(org,
hg18 = {
warning("No NCBI RefSeq Genome annotation for Homo ",
"sapiens hg18! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
knownToRefSeq=
.getUcscTblTpl("knownToRefSeq",what),
knownCanonical=
.getUcscTblTpl("knownCanonical",what)
))
},
hg19 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
hg38 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
mm9 = {
warning("No NCBI RefSeq Genome annotation for Mus ",
"musculus mm9! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
knownToRefSeq=
.getUcscTblTpl("knownToRefSeq",what),
knownCanonical=
.getUcscTblTpl("knownCanonical",what),
knownToEnsembl=
.getUcscTblTpl("knownToEnsembl",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
mm10 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
rn5 = {
warning("No NCBI RefSeq Genome annotation for Rattus ",
"norvegicus rn5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
rn6 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
dm3 = {
warning("No NCBI RefSeq Genome annotation for Drosophila ",
"melanogaster dm3! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
dm6 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
danrer7 = {
warning("No NCBI RefSeq Genome annotation for Danio ",
"rerio danrer7! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
danrer10 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
danrer11 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
pantro4 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro4! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
pantro5 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
pantro6 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
},
susscr3 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v3! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
susscr11 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v11! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
equcab2 = {
warning("No NCBI RefSeq Genome annotation for Equus cabalus v2! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(list(
refFlat=.getUcscTblTpl("refFlat",what),
ensemblToGeneName=
.getUcscTblTpl("ensemblToGeneName",what),
ensemblSource=
.getUcscTblTpl("ensemblSource",what)
))
},
equcab3 = {
return(list(
ncbiRefSeq=.getUcscTblTpl("ncbiRefSeq",what)
))
}
)
}
.getUcscQueryNcbiGene <- function(org) {
switch(org,
hg18 = {
warning("No NCBI RefSeq Genome annotation for Homo ",
"sapiens hg18! Will use UCSC RefSeq instead...",
immediate.=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`,",
"'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`"))
},
hg19 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
hg38 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
mm9 = {
warning("No NCBI RefSeq Genome annotation for Mus ",
"musculus mm9! Will use UCSC RefSeq instead...",
immediate.=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 `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`"))
},
mm10 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
rn5 = {
warning("No NCBI RefSeq Genome annotation for Rattus ",
"norvegicus rn5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
rn6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
dm3 = {
warning("No NCBI RefSeq Genome annotation for Drosophila ",
"melanogaster dm3! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
dm6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
danrer7 = {
warning("No NCBI RefSeq Genome annotation for Danio ",
"rerio danrer7! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
danrer10 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
danrer11 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
pantro4 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro4! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
pantro5 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
pantro6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
susscr3 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v3! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
susscr11 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v11! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
equcab2 = {
warning("No NCBI RefSeq Genome annotation for Equus cabalus v2! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`gene_id`,",
"`gc_content`,`strand`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"refFlat.chrom AS `chromosome`,",
"`txStart` AS `start`,",
"`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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
equcab3 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `gene_id`,",
"0 AS `gc_content`,",
"`strand` AS `strand`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
}
)
}
.getUcscQueryNcbiTranscript <- function(org) {
switch(org,
hg18 = {
warning("No NCBI RefSeq Genome annotation for Homo ",
"sapiens hg18! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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",
"ORDER BY `chromosome`, `start`"))
},
hg19 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
hg38 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
mm9 = {
warning("No NCBI RefSeq Genome annotation for Mus ",
"musculus mm9! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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",
"ORDER BY `chromosome`,`start`"))
},
mm10 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
rn5 = {
warning("No NCBI RefSeq Genome annotation for Rattus ",
"norvegicus rn5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
rn6 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
dm3 = {
warning("No NCBI RefSeq Genome annotation for Drosophila ",
"melanogaster dm3! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
dm6 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
danrer7 = {
warning("No NCBI RefSeq Genome annotation for Danio ",
"rerio danrer7! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
danrer10 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
danrer11 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
pantro4 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro4! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
pantro5 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
pantro6 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
susscr3 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v3! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
susscr11 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v11! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
equcab2 = {
warning("No NCBI RefSeq Genome annotation for Equus cabalus v2! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT refFlat.chrom AS `chromosome`,",
"refFlat.txStart AS `start`,",
"refFlat.txEnd AS `end`,",
"refFlat.name AS `transcript_id`,",
"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 `transcript_id`",
"ORDER BY `chromosome`,`start`"))
},
equcab3 = {
return(paste("SELECT `chrom` AS `chromosome`,",
"`txStart` AS `start`,",
"`txEnd` AS `end`,",
"`name` AS `transcript_id`,",
"`strand` AS `strand`,",
"name2 AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `transcript_id`",
"ORDER BY `chromosome`,`start`"))
}
)
}
.getUcscQueryNcbiExon <- function(org) {
switch(org,
hg18 = {
warning("No NCBI RefSeq Genome annotation for Homo ",
"sapiens hg18! Will use UCSC RefSeq instead...",
immediate.=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`,",
"'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`"))
},
hg19 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
hg38 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
mm9 = {
warning("No NCBI RefSeq Genome annotation for Mus ",
"musculus mm9! Will use UCSC RefSeq instead...",
immediate.=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 `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`"))
},
mm10 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
rn5 = {
warning("No NCBI RefSeq Genome annotation for Rattus ",
"norvegicus rn5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
rn6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
dm3 = {
warning("No NCBI RefSeq Genome annotation for Drosophila ",
"melanogaster dm3! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
dm6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
danrer7 = {
warning("No NCBI RefSeq Genome annotation for Danio ",
"rerio danrer7! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
danrer10 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
danrer11 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
pantro4 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro4! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
pantro5 = {
warning("No NCBI RefSeq Genome annotation for Pan troglodytes ",
"pantro5! Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
pantro6 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
},
susscr3 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v3! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
susscr11 = {
warning("No NCBI RefSeq Genome annotation for Sus scrofa v11! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
equcab2 = {
warning("No NCBI RefSeq Genome annotation for Equus cabalus v2! ",
"Will use UCSC RefSeq instead...",
immediate.=TRUE)
return(paste("SELECT `chromosome`,`start`,`end`,`exon_id`,",
"`strand`,`gene_id`,`gene_name`,`biotype` FROM",
"(SELECT MAX(`txEnd` - `txStart`) AS `width`,",
"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_name`",
"ORDER BY `chromosome`,`start`) AS tmp"))
},
equcab3 = {
return(paste(
"SELECT `chrom` AS `chromosome`,",
"`exonStarts` AS `start`,",
"`exonEnds` AS `end`,",
"`name` AS `exon_id`,",
"`strand` AS `strand`,",
"`name` AS `gene_id`,",
"`name2` AS `gene_name`,",
"'NA' AS `biotype`",
"FROM `ncbiRefSeq`",
"GROUP BY `gene_name`",
"ORDER BY `chromosome`,`start`"
))
}
)
}
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