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gffFile <- system.file("extdata", "GFF3_files", "a.gff3",
package="txdbmaker")
gtfFile <- system.file("extdata", "GTF_files",
"GCA_002204515.1_AaegL5.0_genomic.gtf.gz",
package="txdbmaker")
flyFile <- system.file("extdata","GFF3_files","dmel-1000-r5.11.filtered.gff",
package="txdbmaker")
## bad bacterial GFFs require use of special argument to ignore most of data.
gffB <- system.file("extdata", "GFF3_files",
"GCF_000020065.1_ASM2006v1_genomic.gff",
package="txdbmaker")
## Test that outputs match what is expected. ## BOOM
test_makeTxDbFromGFF <- function(){
## wanted
gffDBFile <- system.file("extdata", "GFF3_files", "a.sqlite",
package="txdbmaker")
txdb_gff <- loadDb(gffDBFile)
## generated
txdb1 <- makeTxDbFromGFF(file=gffFile,
dataSource="partial GFF file for Tomatoes for testing",
organism="Solanum lycopersicum",
circ_seqs=character(0))
## test
checkTrue(GenomicFeatures:::compareTxDbs(txdb1, txdb_gff))
## wanted
gtfDBFile <- system.file("extdata", "GTF_files",
"GCA_002204515.1_AaegL5.0_genomic.sqlite",
package="txdbmaker")
txdb_gtf <- loadDb(gtfDBFile)
## generated
chrominfo <- data.frame(chrom="MF194022.1", length=16790, is_circular=TRUE)
dataSource <- paste0("https://ftp.ncbi.nlm.nih.gov/genomes/all/",
"GCA/002/204/515/GCA_002204515.1_AaegL5.0/",
"GCA_002204515.1_AaegL5.0_genomic.gtf.gz")
organism <- "Aedes aegypti"
metadata <- data.frame(name="Genome", value="AaegL5.0")
txdb2 <- makeTxDbFromGFF(gtfFile, dataSource=dataSource, organism=organism,
chrominfo=chrominfo, metadata=metadata)
## test
checkTrue(GenomicFeatures:::compareTxDbs(txdb2, txdb_gtf))
## wanted
flyDBFile <- system.file("extdata", "GFF3_files",
"dmel-1000-r5.11.filtered.sqlite",
package="txdbmaker")
txdb_fly <- loadDb(flyDBFile)
txdb3 <- makeTxDbFromGFF(file=flyFile,
dataSource="gff file from flybase",
organism="Drosophila melanogaster",
circ_seqs=character(0))
checkTrue(GenomicFeatures:::compareTxDbs(txdb3, txdb_fly))
## test for broken NCBI bacterial GFFs (that only seem to have
## reliable gene info and little else)
chrominfoBac <- data.frame(chrom = c('NC_011025.1'),
length=c(830000), ## placeholder = iow it big enough
is_circular=c(TRUE))
## mostly I want to see if if can run this:
txdb_bac <- makeTxDbFromGFF(file = gffB,
chrominfo = chrominfoBac,
dataSource = "NCBI",
organism = "Metamycoplasma arthritidis")
## Tests
checkTrue(class(txdb_bac) == "TxDb")
checkEquals(length(transcripts(txdb_bac)), 672)
}
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