2011年4月14日星期四

checking the seed files of BSgenome data packages forged by the Bioconductor project

To make a BSgenome data package, you need to prepare seed file. So, checking the seed files of others may be to right way for you, if you have no idea about it.

Here some codes from manu of BSgenome package can help you to check the seed files used for the package forged by the Bioconductor project.

#############################################################################
# check the seed files from GentlemanLab
> library(BSgenome)
Loading required package: IRanges

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: GenomicRanges
Loading required package: Biostrings
> seed_files<-system.file("extdata", "GentlemanLab", package="BSgenome") > list.files(seed_files, pattern="-seed$")
[1] "BSgenome.Amellifera.BeeBase.assembly4-seed"
[2] "BSgenome.Amellifera.UCSC.apiMel2-seed"
[3] "BSgenome.Athaliana.TAIR.01222004-seed"
[4] "BSgenome.Athaliana.TAIR.04232008-seed"
[5] "BSgenome.Athaliana.TAIR.TAIR9-seed"
[6] "BSgenome.Btaurus.UCSC.bosTau3-seed"
[7] "BSgenome.Btaurus.UCSC.bosTau4-seed"
[8] "BSgenome.Celegans.UCSC.ce2-seed"
[9] "BSgenome.Celegans.UCSC.ce6-seed"
[10] "BSgenome.Cfamiliaris.UCSC.canFam2-seed"
[11] "BSgenome.Dmelanogaster.UCSC.dm2-seed"
[12] "BSgenome.Dmelanogaster.UCSC.dm3-seed"
[13] "BSgenome.Drerio.UCSC.danRer5-seed"
[14] "BSgenome.Drerio.UCSC.danRer6-seed"
[15] "BSgenome.Drerio.UCSC.danRer7-seed"
[16] "BSgenome.Ecoli.NCBI.20080805-seed"
[17] "BSgenome.Gaculeatus.UCSC.gasAcu1-seed"
[18] "BSgenome.Ggallus.UCSC.galGal3-seed"
[19] "BSgenome.Hsapiens.UCSC.hg17-seed"
[20] "BSgenome.Hsapiens.UCSC.hg18-seed"
[21] "BSgenome.Hsapiens.UCSC.hg19-seed"
[22] "BSgenome.influenza.NCBI.20100628-seed"
[23] "BSgenome.Mmusculus.UCSC.mm8-seed"
[24] "BSgenome.Mmusculus.UCSC.mm9-seed"
[25] "BSgenome.Ptroglodytes.UCSC.panTro2-seed"
[26] "BSgenome.Rnorvegicus.UCSC.rn4-seed"
[27] "BSgenome.Scerevisiae.UCSC.sacCer1-seed"
[28] "BSgenome.Scerevisiae.UCSC.sacCer2-seed"
> seed_files
[1] "/ebio/abt6/jmao/bin/R-2.13/Rpacks/BSgenome/extdata/GentlemanLab"
> rn4_seed<-list.files(seed_files, pattern="rn4", full.names=TRUE) > cat(readLines(rn4_seed), sep="\n")
Package: BSgenome.Rnorvegicus.UCSC.rn4
Title: Rattus norvegicus (Rat) full genome (UCSC version rn4)
Description: Rattus norvegicus (Rat) full genome as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects.
Version: 1.3.17
organism: Rattus norvegicus
species: Rat
provider: UCSC
provider_version: rn4
release_date: Nov. 2004
release_name: Baylor College of Medicine HGSC v3.4
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/rn4/bigZips/
organism_biocview: Rattus_norvegicus
BSgenomeObjname: Rnorvegicus
seqnames: paste("chr", c(1:20, "X", "M", "Un", paste(c(1:20, "X", "Un"), "_random", sep="")), sep="")
circ_seqs: "chrM"
mseqnames: paste("upstream", c("1000", "2000", "5000"), sep="")
nmask_per_seq: 4
SrcDataFiles1: sequences: chromFa.tar.gz, upstream1000.fa.gz, upstream2000.fa.gz, upstream5000.fa.gz
from http://hgdownload.cse.ucsc.edu/goldenPath/rn4/bigZips/
SrcDataFiles2: AGAPS masks: all the chr*_gap.txt.gz files from ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/database/
RM masks: http://hgdownload.cse.ucsc.edu/goldenPath/rn4/bigZips/chromOut.tar.gz
TRF masks: http://hgdownload.cse.ucsc.edu/goldenPath/rn4/bigZips/chromTrf.tar.gz
PkgExamples: Rnorvegicus
seqlengths(Rnorvegicus)
Rnorvegicus$chr1 # same as Rnorvegicus[["chr1"]]
seqs_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Rnorvegicus.UCSC.rn4/seqs
masks_srcdir: /home/hpages/BSgenomeForge/srcdata/BSgenome.Rnorvegicus.UCSC.rn4/masks
>

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