[Bioc-sig-seq] SRAdb and getFastq

[Martin Morgan]

On 03/04/2011 10:10 AM, Sean Davis wrote:
> On Mar 4, 2011 11:15 AM, "kirti prakash" <kirtiprakash3.14 at gmail.com> wrote:
>>
>> Hi,
>>
>> I wanted to get fastq files associated with some SRA
>>
>> So I was going through the following SRAdb vignettes
>>
> http://bioconductor.org/packages/2.6/bioc/vignettes/SRAdb/inst/doc/SRAdb.pdf
>>
>> <
> http://bioconductor.org/packages/2.6/bioc/vignettes/SRAdb/inst/doc/SRAdb.pdf
>> I
>> am able to run most of the commands except the ones in section 3.5(which I
>> actually need)
>>
>> The error I am getting is
>> getFastq (in_acc=c("SRR000648","SRR000657"), sra_con=sra_con,
>> destdir=getwd())
>> Error: could not find function "getFastq"
>>
>> getFastq
>> Error: object 'getFastq' not found
>>
>> Similarly for listFastq and getFastInfo functions
>>
>> I am wondering if I am missing something ?
> 
> Unfortunately, you are not.  NCBI has removed the fastq files from its site,
> so these functions have been removed from sraDB.

Also, I think your version of R and SRAdb don't match (biocLite
installed SRAdb version 1.2.1 under R-2.11.1). A better bet is to update
to R-2.12.2, update your installed packages

  http://bioconductor.org/install/

and use the current vignette, available with

  browseVignettes("SRAdb")

This won't make getFastq magically appear, but it will make the software
and vignette function in a consistent way.

Martin

> 
> Sean
> 
>> Best regards,
>>
>> Kirti Prakash
>>
>> sessionInfo()
>> R version 2.11.1 (2010-05-31)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
>>  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
>>  [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
>>  [7] LC_PAPER=en_US.iso885915       LC_NAME=C
>>  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] SRAdb_1.4.1   graph_1.28.0  RSQLite_0.9-2 DBI_0.2-5
>>
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.8.0   GEOquery_2.16.3 RCurl_1.4-3     tools_2.11.1
>> [5] XML_3.1-0
>>
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>>
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> 
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