SRAdb queries for NIH Hackathon

library(SRAdb)

## Loading required package: RSQLite
## Loading required package: DBI
## Loading required package: graph
## Loading required package: RCurl
## Loading required package: bitops
## Setting options('download.file.method.GEOquery'='curl')

srafile = 'SRAmetadb.sqlite'
if(!file.exists(srafile)) srafile <<- getSRAdbFile()

con = dbConnect(SQLite(),srafile)

rs = dbGetQuery(con,"
  select *
  from sra_ft where
         sample_attribute MATCH 'MCF7 OR MCF-7' AND
         taxon_id=9606 AND
         library_source='TRANSCRIPTOMIC'")

dim(rs)

## [1] 834  74

write.table(rs,file='MCF7.accessionlist.txt',sep="\t",row.names=FALSE,quote=FALSE)
system('s3cmd put MCF7.accessionlist.txt s3://sdavis.nci.nih.gov')