## ----install-0, eval=FALSE, echo=TRUE----------------------------------------- # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("metaseqR2") ## ----load-0, eval=TRUE, echo=FALSE, tidy=FALSE, message=FALSE, warning=FALSE---- library(metaseqR2) ## ----example-1, eval=TRUE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- library(metaseqR2) buildDir <- file.path(tempdir(),"test_anndb") dir.create(buildDir) # The location of the custom database myDb <- file.path(buildDir,"testann.sqlite") # Since we are using Ensembl, we can also ask for a version organisms <- list(mm39=115) sources <- ifelse(.Platform$OS.type=="unix",c("ensembl","refseq"),"ensembl") # If the example is not running in a multicore system, rc is ignored #buildAnnotationDatabase(organisms,sources,forceDownload=FALSE,db=myDb,rc=0.5) ## ----example-2, eval=FALSE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # # Load standard annotation based on gene body coordinates # genes <- loadAnnotation(genome="mm39",refdb="ensembl",level="gene",type="gene", # db=myDb) # genes # # # Load standard annotation based on 3' UTR coordinates # utrs <- loadAnnotation(genome="mm39",refdb="ensembl",level="gene",type="utr", # db=myDb) # utrs # # # Load summarized exon annotation based used with RNA-Seq analysis # sumEx <- loadAnnotation(genome="mm39",refdb="ensembl",level="gene",type="exon", # summarized=TRUE,db=myDb) # sumEx # # # Load standard annotation based on gene body coordinates from RefSeq # if (.Platform$OS.type=="unix") { # refGenes <- loadAnnotation(genome="mm39",refdb="refseq",level="gene", # type="gene",db=myDb) # refGenes # } ## ----example-3, eval=FALSE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # # Load standard annotation based on gene body coordinates # genes <- loadAnnotation(genome="mm39",refdb="ensembl",level="gene",type="gene", # db=myDb,asdf=TRUE) # head(genes) ## ----example-4, eval=FALSE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # # Setup a temporary directory to download files etc. # customDir <- file.path(tempdir(),"test_custom") # dir.create(customDir) # # # Convert from GenePred to GTF - Unix/Linux only! # if (.Platform$OS.type == "unix" && !grepl("^darwin",R.version$os)) { # # Download data from UCSC # goldenPath="http://hgdownload.cse.ucsc.edu/goldenPath/" # # Gene annotation dump # download.file(paste0(goldenPath,"eboVir3/database/ncbiGene.txt.gz"), # file.path(customDir,"eboVir3_ncbiGene.txt.gz")) # # Chromosome information # download.file(paste0(goldenPath,"eboVir3/database/chromInfo.txt.gz"), # file.path(customDir,"eboVir3_chromInfo.txt.gz")) # # # Prepare the build # chromInfo <- read.delim(file.path(customDir,"eboVir3_chromInfo.txt.gz"), # header=FALSE) # chromInfo <- chromInfo[,1:2] # rownames(chromInfo) <- as.character(chromInfo[,1]) # chromInfo <- chromInfo[,2,drop=FALSE] # # # Coversion from genePred to GTF # genePredToGtfEnv <- Sys.getenv("GENEPREDTOGTF_BINARY") # if (genePredToGtfEnv == "") { # genePredToGtf <- file.path(customDir,"genePredToGtf") # } else { # genePredToGtf <- file.path(genePredToGtfEnv) # } # if (!file.exists(genePredToGtf)) { # download.file( # "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf", # genePredToGtf # ) # system(paste("chmod 775",genePredToGtf)) # } # gtfFile <- file.path(customDir,"eboVir3.gtf") # tmpName <- file.path(customDir,paste(format(Sys.time(),"%Y%m%d%H%M%S"), # "tgtf",sep=".")) # command <- paste0( # "zcat ",file.path(customDir,"eboVir3_ncbiGene.txt.gz"), # " | ","cut -f2- | ",genePredToGtf," file stdin ",tmpName, # " -source=eboVir3"," -utr && grep -vP '\t\\.\t\\.\t' ",tmpName," > ", # gtfFile # ) # system(command) # # # Build with the metadata list filled (you can also provide a version) # buildCustomAnnotation( # gtfFile=gtfFile, # metadata=list( # organism="eboVir3_test", # source="ucsc_test", # chromInfo=chromInfo # ), # db=myDb # ) # # # Try to retrieve some data # eboGenes <- loadAnnotation(genome="eboVir3_test",refdb="ucsc_test", # level="gene",type="gene",db=myDb) # eboGenes # } ## ----example-5, eval=FALSE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # if (.Platform$OS.type == "unix") { # # Gene annotation dump # download.file(paste0(goldenPath,"gadMor1/database/augustusGene.txt.gz"), # file.path(customDir,"gadMori1_augustusGene.txt.gz")) # # Chromosome information # download.file(paste(goldenPath,"gadMor1/database/chromInfo.txt.gz",sep=""), # file.path(customDir,"gadMori1_chromInfo.txt.gz")) # # # Prepare the build # chromInfo <- read.delim(file.path(customDir,"gadMori1_chromInfo.txt.gz"), # header=FALSE) # chromInfo <- chromInfo[,1:2] # rownames(chromInfo) <- as.character(chromInfo[,1]) # chromInfo <- chromInfo[,2,drop=FALSE] # # # Coversion from genePred to GTF # genePredToGtf <- file.path(customDir,"genePredToGtf") # if (!file.exists(genePredToGtf)) { # download.file( # "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf", # genePredToGtf # ) # system(paste("chmod 775",genePredToGtf)) # } # gtfFile <- file.path(customDir,"gadMori1.gtf") # tmpName <- file.path(customDir,paste(format(Sys.time(),"%Y%m%d%H%M%S"), # "tgtf",sep=".")) # command <- paste0( # "zcat ",file.path(customDir,"gadMori1_augustusGene.txt.gz"), # " | ","cut -f2- | ",genePredToGtf," file stdin ",tmpName, # " -source=gadMori1"," -utr && grep -vP '\t\\.\t\\.\t' ",tmpName," > ", # gtfFile # ) # system(command) # # # Build with the metadata list filled (you can also provide a version) # buildCustomAnnotation( # gtfFile=gtfFile, # metadata=list( # organism="gadMor1_test", # source="ucsc_test", # chromInfo=chromInfo # ), # db=myDb # ) # # # Try to retrieve some data # gadGenes <- loadAnnotation(genome="gadMor1_test",refdb="ucsc_test", # level="gene",type="gene",db=myDb) # gadGenes # } ## ----example-6, eval=FALSE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # # Gene annotation dump from Ensembl # download.file(paste0("ftp://ftp.ensembl.org/pub/release-98/gtf/", # "dasypus_novemcinctus/Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz"), # file.path(customDir,"Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz")) # # # Chromosome information will be provided from the following BAM file # # available from Ensembl. We have noticed that when using Windows as the OS, # # a remote BAM files cannot be opened by scanBamParam, so for this example, # # chromosome length information will not be available when running in Windows. # bamForInfo <- NULL # if (.Platform$OS.type == "unix") # bamForInfo <- paste0("ftp://ftp.ensembl.org/pub/release-98/bamcov/", # "dasypus_novemcinctus/genebuild/Dasnov3.broad.Ascending_Colon_5.1.bam") # # # Build with the metadata list filled (you can also provide a version) # buildCustomAnnotation( # gtfFile=file.path(customDir,"Dasypus_novemcinctus.Dasnov3.0.98.gtf.gz"), # metadata=list( # organism="dasNov3_test", # source="ensembl_test", # chromInfo=bamForInfo # ), # db=myDb # ) # # # Try to retrieve some data # dasGenes <- loadAnnotation(genome="dasNov3_test",refdb="ensembl_test", # level="gene",type="gene",db=myDb) # dasGenes ## ----example-7, eval=FALSE, echo=TRUE, tidy=FALSE, message=TRUE, warning=FALSE---- # organisms <- list( # hg18=54, # hg19=75, # hg38=114:115, # mm9=54, # mm10=102, # mm39=114:115, # rn5=77, # rn6=114:115, # dm3=77, # dm6=114:115, # danrer7=77, # danrer10=80, # danrer11=114:115, # pantro4=80, # pantro5=114:115, # susscr3=80, # susscr11=114:115, # equcab2=77 # ) # # sources <- c("ensembl","ucsc","refseq") # # buildAnnotationDatabase(organisms,sources,forceDownload=FALSE,rc=0.5) ## ----pseudo-1, eval=TRUE, echo=TRUE, message=TRUE, warning=FALSE-------------- annotation <- list( gtf="PATH_TO_GTF", organism="ORGANISM_NAME", source="SOURCE_NAME", chromInfo="CHROM_INFO" ) ## ----si-1, eval=TRUE, echo=TRUE----------------------------------------------- sessionInfo()