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Question: SRAdb "outdated" sqlite db
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gravatar for Nicolas Delhomme
14 months ago by
Sweden
Nicolas Delhomme320 wrote:

Hej Jack Zhu and Sean Davis!

I wanted to retrieve data that have recently been submitted (end of august) to the SRA, but I cannot do it using SRAdb, as the database I can fetch using getSRAdbFile() is "outdated", dating from early august: c("schema version", "creation timestamp")c("1.0", "2016-08-06 00:25:18") It corresponds to this file: 'https://dl.dropboxusercontent.com/u/51653511/SRAmetadb.sqlite.gz'

I could not find the info, but I suppose updating this db is something you do manually? How often do you do it? And is it something you could share the code to, so that end-user could do it too?

Thanks in advance for your answer,

Cheers,

Nico

 

My session info:

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] SRAdb_1.30.0         RCurl_1.95-4.8       bitops_1.0-6        
[4] graph_1.50.0         BiocGenerics_0.18.0  RSQLite_1.0.0       
[7] DBI_0.5-1            BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] httr_1.2.1      R6_2.1.3        tools_3.3.1     GEOquery_2.38.4 Biobase_2.32.0 
[6] stats4_3.3.1    XML_3.98-1.4   

ADD COMMENTlink modified 14 months ago by Sean Davis21k • written 14 months ago by Nicolas Delhomme320
0
gravatar for Sean Davis
14 months ago by
Sean Davis21k
United States
Sean Davis21k wrote:

Thanks for the report.  Should be fixed now. Yes, we have code, but it is not packaged up in a user-friendly way.  The data are actually processed into a local mysql database and then the ETL and packaging into SQLite are done from there.  This is for historical reasons and we simply haven't had the resources to unravel it.

ADD COMMENTlink written 14 months ago by Sean Davis21k
Hej Sean! Thanks! I'm managing the bioinformatics facility at the Umeå Plant Science Centre and we are planning to screen the SRA using SRAdb for datasets of interests that we could add to our Genome Browser resource plantgenie.org) on a regular basis. As such, we could contribute running the SQLite database generation if you're interested. Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme, PhD UPSC bioinformatics facility Manager Umeå Plant Science Center, Swedish University for Agricultural Sciences (SLU) and Umeå University Tel: +46 90 786 5478 Email: nicolas.delhomme@umu.se SLU - Umeå universitet Umeå S-901 87 Sweden --------------------------------------------------------------- > On 22 Sep 2016, at 16:20, Sean Davis [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User Sean Davis wrote Answer: SRAdb "outdated" sqlite db: > > > Thanks for the report. Should be fixed now. Yes, we have code, but it is not packaged up in a user-friendly way. The data are actually processed into a local mysql database and then the ETL and packaging into SQLite are done from there. This is for historical reasons and we simply haven't had the resources to unravel it. > > > Post tags: sradb, sqlite, outdated > > You may reply via email or visit A: SRAdb "outdated" sqlite db >
ADD REPLYlink written 14 months ago by Nicolas Delhomme320
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