Package: BSgenome.Mfascicularis.NCBI.5.0
Title: Full genome sequences for Macaca fascicularis (Macaca_fascicularis_5.0)
Description: Full genome sequences for Macaca fascicularis (long-tailed macaque) as provided by NCBI (Macaca_fascicularis_5.0, 2013-06-12) and stored in Biostrings objects.
Version: 1.4.2
organism: Macaca fascicularis
common_name: long-tailed macaque
provider: NCBI
provider_version: Macaca_fascicularis_5.0
release_date: 2013-06-12
release_name: Macaca_fascicularis_5.0
source_url: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000364345.1_Macaca_fascicularis_5.0/
organism_biocview: Macaca_fascicularis
BSgenomeObjname: Mfascicularis
seqnames:
circ_seqs: "MT"
SrcDataFiles: GCF_000364345.1_Macaca_fascicularis_5.0_genomic.fna.gz from ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF_000364345.1_Macaca_fascicularis_5.0/
PkgExamples: genome$MFA1  # same as genome[["MFA1"]]
	.
	## ---------------------------------------------------------------------
	## About the ordering of the sequences
	## ---------------------------------------------------------------------
	## The sequences in BSgenome object 'genome' are ordered like in the
	## assembly report at the following URL
	url <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000364345.1.assembly.txt"
	## except that the MT sequence was moved from the last position to the
	## position between the chromosomes (MFA* sequences) and the scaffolds
	## (Scaffold* sequences):
	SequenceName <- read.table(url, sep="\t", stringsAsFactors=FALSE)[[1]]
	target_seqlevels <- SequenceName[c(1:21, 7601, 22:7600)]
	stopifnot(identical(seqlevels(genome), target_seqlevels))
seqs_srcdir: /fh/fast/morgan_m/BioC/BSgenomeForge/srcdata/BSgenome.Mfascicularis.NCBI.5.0/seqs
seqfile_name: Macaca_fascicularis_5.0.sorted.2bit