[Bioc-sig-seq] ShortRead, readAligned() and qa()

[Ivan Gregoretti]

Hi Martin,

Your suggestion of passing the relevant pattern as argument to qa() like this

qa(sp, pattern=".*_export.txt.gz")

solved the problem.

Thank you,

Ivan

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878



On Tue, Jun 9, 2009 at 7:43 AM, Martin Morgan<mtmorgan at fhcrc.org> wrote:
> Ivan Gregoretti <ivangreg at gmail.com> writes:
>
>> Hello everybody,
>>
>> Can qa() work on compressed *_export.txt files?
>>
>>
>>
>> The function readAligned() is very smart because it does not care if the
>> export file is plain or compressed. You just do
>>
>> aln <- readAligned(sp, fileNamePattern)
>>
>> and the lane is loaded up.
>>
>> I tried to run qa() on a directory with compressed export files and I got:
>>
>>> sp <- SolexaPath(experimentPath=myExperimentPath,
>> analysisPath=myAnalysisPath)
>>> sp
>> class: SolexaPath
>> experimentPath: /data/igregore/all/runs/090529/
>> dataPath: NA
>> scanPath: NA
>> imageAnalysisPath: NA
>> baseCallPath: NA
>> analysisPath: GERALD_01-06-20...
>>> qa <- qa(sp)
>> Error: Input/Output
>>   no input files found
>>  dirPath: /data/igregore/all/runs/090529/GERALD_01-06-2009_niddk/
>>   pattern: .*_export.txt$
>>
>>
>> I guess that qa()'s inability to read .txt.gz is a feature rather than a
>> bug. If so, would you please consider adding this capability on a future
>> ShortRead release?
>
> Hi Ivan -- I think you should be able to specify a pattern
>
>  qa(sp, pattern=".*_export.txt.gz")
>
> and failing that provide a dirfull direcotry path
>
>  qa(analysisPath(sp), pattern=".*_export.txt.gz")
>
> let me know if that does not work.
>
> Martin
>
>
>> Thank you,
>>
>> Ivan
>>
>>> sessionInfo()
>> R version 2.9.0 (2009-04-17)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] ShortRead_1.2.0   lattice_0.17-22   BSgenome_1.12.0   Biostrings_2.12.1
>> [5] IRanges_1.2.0
>>
>> loaded via a namespace (and not attached):
>> [1] Biobase_2.4.1 grid_2.9.0    hwriter_1.1
>>
>>
>> Ivan Gregoretti, PhD
>> National Institute of Diabetes and Digestive and Kidney Diseases
>> National Institutes of Health
>> 5 Memorial Dr, Building 5, Room 205.
>> Bethesda, MD 20892. USA.
>> Phone: 1-301-496-1592
>> Fax: 1-301-496-9878
>>
>>       [[alternative HTML version deleted]]
>>
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>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>