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

[Martin Morgan]

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