get.id <-
function (x, id.type = "locus"){
if(! id.type %in% c('locus','protein','transcript') )
stop('ERROR: Unknown ID-type')
x2 = paste(x, sep = ", ", collapse = "', '")
x2 = paste("('", x2, "')", sep = "")
## define query
if(x[1] == "*"){
query <- paste("
SELECT
gen.gene_id, gen.gene, gen.protein_id, gen.transcript_id, gen.gene_biotype
FROM GENES gen ORDER BY gen.gene_id", sep =" ")
}
else if(id.type == "locus"){
query <- paste("
SELECT
gen.gene_id, gen.gene
FROM GENES gen
WHERE gen.gene IN", x2, "ORDER BY gen.gene", sep = " ")
}
else if(id.type == "transcript"){
query <- paste("
SELECT
gen.gene_id, gen.transcript_id
FROM GENES gen
WHERE gen.transcript_id IN", x2, "ORDER BY gen.gene_id", sep = " ")
}
else if(id.type == "protein"){
query <- paste("
SELECT
gen.gene_id, gen.protein_id
FROM GENES gen
WHERE gen.protein_id IN", x2, "ORDER BY gen.gene_id", sep = " ")
}
out <- dbGetQuery(.datacache$con, query)
return(out)
}
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