[Bioc-devel] SRAdb missing runs

[Sean Davis]

Sorry, Malcolm.

We'll look into it.  Thanks for the report.

Sean


On Wed, Sep 14, 2011 at 5:09 PM, Cook, Malcolm <MEC at stowers.org> wrote:
> 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
>
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