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?

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

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