### INFO: R Script
### DATE: 29.04.2013
### AUTHOR: Vedran Franke
rm(list=ls())
# {0} TEST DATA
#/{0} TEST DATA
# {1} LIBRARIES
lib.path=file.path(Sys.getenv('HOME'),'bin/MyLib/RFun')
source(file.path(lib.path, 'FileLoader.R'))
source(file.path(lib.path, 'FormatConverters.R'))
source(file.path(lib.path, 'BamWorkers.R'))
source(file.path(lib.path, 'ScanLib.R'))
library(data.table)
library(biomaRt)
library(GEOquery)
library(doMC)
library(sra)
library(SRAdb)
#/{1} LIBRARIES
# {2} CODE
# {{1}} FUNCTIONS
#/{{1}} FUNCTIONS
# {{2}} INPUT VARIABLES
# {{{1}}} PATH VARIABLES
outdir='/data/akalin/Base/AccessoryData/'
sradb = '~/Tmp/SRAmetadb.sqlite'
#/{{{1}}} PATH VARIABLES
# {{{2}}} SCRIPT PARAMS
outname='GSE41091_Nekrasov_2012_NSMB_CTCF_ChipSeq'
registerDoMC(20)
#/{{{2}}} SCRIPT PARAMS
#/{{2}} INPUT VARIABLES
# {{3}} MAIN
outpath = file.path(outdir, outname, 'Raw','SRA')
dir.create(outpath, showWarnings=FALSE, recursive=TRUE)
id = unlist(strsplit(outname,'_'))[1]
geo = getGEO(exps)[[1]]
p = pData(geo)
d = data.frame(sample=p$title, id=basename(p$supplementary_file_1))
if(!file.exists(sradb))
getSRAdbFile(destdir=dirname(sradb))
con = dbConnect(dbDriver("SQLite"),sradb)
sra = getSRAinfo(in_acc=d$id, sra_con=con)
sra = sra[c('experiment','ftp')]
m = merge(d, sra, by.x='id', by.y='experiment')
foreach(i = 1:nrow(m))%dopar%{
print(i)
file=m$ftp[i]
download.file(file, file.path(outpath, paste(m$sample[i], 'sra', sep='.')))
}
#/{{3}} MAIN
#/{2} CODE
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