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<[email protected]> wrote: > Ivan Gregoretti <[email protected]> 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]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > -- > 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 > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
