[Bioc-devel] SRAdb missing runs

Hi Sean, Jack, and fellow SRAdb users,

Sean, I failed to cc: you 1st time around. ?Perhaps you have a suggestion for me....???

I remain perplexed as to why selected SRA runs fail to appear in SRAdb.

Does anyone else have some experience/advice in this.

Thanks much,

~Malcolm


-----Original Message-----
From: Cook, Malcolm
Sent: Friday, September 09, 2011 4:15 PM
To: 'bioc-devel at r-project.org'; 'zhujack at mail.nih.gov'
Subject: SRAdb missing runs

Hi Jack and other SRAdb users,

I find at least one SRA run missing from the sqlite database obtained from a fresh `getSRAdbFile()`

SRR074430 is present in the SRA http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=viewer&m=data&s=viewer&run=SRR074430

but directly querying the sqlite3 database fails to find it:

sqlite3 -list SRAmetadb.sqlite "select study_accession, submission_accession, sample_accession, experiment_accession, run_accession, ?sample_alias from sra ?where run_accession in ('SRR031766','SRR031767','SRR074430')"
SRP001537|SRA010243|SRS008471|SRX014483|SRR031766|S2_DRSC_CG10128_RNAi-1
SRP001537|SRA010243|SRS008471|SRX014483|SRR031767|S2_DRSC_CG10128_RNAi-1

Can anyone advise me as the origin of this discrepancy, or perhaps fix a misunderstanding I may have in using this resource.

I just downloaded a fresh SRAdbFile... ?here is the "Metadata associate with downloaded file:"

c("schema version", "creation timestamp")c("1.0", "2011-09-03 10:38:16")


Below is a full transcript with SessionInfo(), if it helps.

Thanks!

Malcolm Cook
Computational Biology - Stowers Institute for Medical Research

library('SRAdb')
sqlfile <- getSRAdbFile()

sqlfile <- getSRAdbFile()
trying URL 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
Content type 'text/plain; charset=ISO-8859-1' length 38391904 bytes (36.6 Mb)
opened URL
==================================================
downloaded 36.6 Mb

Unzipping...

Metadata associate with downloaded file:

c("schema version", "creation timestamp")c("1.0", "2011-09-03 10:38:16")

sessionInfo()

sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base

other attached packages:
[1] SRAdb_1.6.0 ? ?RCurl_1.5-0 ? ?bitops_1.0-4.1 graph_1.30.0 ? RSQLite_0.9-4
[6] DBI_0.2-5

loaded via a namespace (and not attached):
[1] Biobase_2.12.2 ?GEOquery_2.19.2 XML_3.4-0 ? ? ? tools_2.13.1

q('no')

bash-3.2$ ? ?sqlite3 -list SRAmetadb.sqlite "select study_accession, submission_accession, sample_accession, experiment_accession, run_accession, ?sample_alias from sra ?where run_accession in ('SRR031766','SRR031767','SRR074430')"
?sqlite3 -list SRAmetadb.sqlite "select study_accession, submission_accession, sample_accession, experiment_accession, run_accession, ?sample_alias from sra ?where run_accession in ('SRR031766','SRR031767','SRR074430')"
SRP001537|SRA010243|SRS008471|SRX014483|SRR031766|S2_DRSC_CG10128_RNAi-1
SRP001537|SRA010243|SRS008471|SRX014483|SRR031767|S2_DRSC_CG10128_RNAi-1