## ----style, echo = FALSE, results = 'asis'------------------------------- BiocStyle::markdown() ## ---- echo=FALSE, results="hide"----------------------------------------- library(knitr) opts_chunk$set(error=FALSE) ## ---- exampleInpProcessing----------------------------------------------- makeinparanoid8ToAHMs <- function(currentMetadata){ baseUrl <- 'http://inparanoid.sbc.su.se/download/current/Orthologs_other_formats' ## Make list of metadata in a helper function meta <- .inparanoidMetadataFromUrl(baseUrl) ## then make AnnotationHubMetadata objects. Map(AnnotationHubMetadata, Description=meta$description, Genome=meta$genome, SourceFile=meta$sourceFile, SourceUrl=meta$sourceUrl, SourceVersion=meta$sourceVersion, Species=meta$species, TaxonomyId=meta$taxonomyId, Title=meta$title, RDataPath=meta$rDataPath, MoreArgs=list( Coordinate_1_based = TRUE, DataProvider = baseUrl, Maintainer = "Marc Carlson ", RDataClass = "SQLiteFile", RDataDateAdded = Sys.time(), RDataVersion = "0.0.1", Recipe = "AnnotationHubData:::inparanoid8ToDbsRecipe", Tags = c("Inparanoid", "Gene", "Homology", "Annotation"))) } ## ---- exampleRecipe------------------------------------------------------ inparanoid8ToDbsRecipe <- function(ahm){ require(AnnotationForge) inputFiles <- metadata(ahm)$SourceFile dbname <- makeInpDb(dir=file.path(inputFiles,""), dataDir=tempdir()) db <- loadDb(file=dbname) outputPath <- file.path(metadata(ahm)$AnnotationHubRoot, metadata(ahm)$RDataPath) saveDb(db, file=outputPath) outputFile(ahm) } ## ----eval=FALSE---------------------------------------------------------- # setClass("BEDFileResource", contains="AnnotationHubResource") # # setMethod(".get1", "BEDFileResource", # function(x, ...) # { # .require("rtracklayer") # yy <- .hub(x) # dat <- rtracklayer::BEDFile(cache(yy)) # rtracklayer::import(dat, format="bed", genome=yy$genome, ...) # }) ## ---- SessionInfo, echo=FALSE-------------------------------------------- sessionInfo()