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
