Thanks, Martin G
On 4/30/09 11:47 AM, "Martin Morgan" <[email protected]> wrote: Hi Gordon -- Gordon Robertson wrote: > Thanks, Martin, > > Given the folder contents, the original pattern would have matched both > 'map' and 'mapstats': > {xhost06}/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq> ll > ... > -rw-rw-r-- 1 rvarhol slx_service 508774 Apr 22 15:52 30WLMAAXX_5.map > -rw-rw-r-- 1 rvarhol slx_service 2 Apr 22 15:52 30WLMAAXX_5.mapstats > ... > > The more specific pattern that you suggested worked: >> readAligned("/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq/", > pattern="^30WLMAAXX_5.map$", type="MAQMap") > class: AlignedRead > length: 9057150 reads; width: 50 cycles > chromosome: 1 1 ... Y Y > position: 2 9 ... 57442746 57443286 > strand: - - ... - - > alignQuality: IntegerQuality > alignData varLabels: nMismatchBestHit mismatchQuality nExactMatch24 > nOneMismatch24 > ... > > Note though that when I specified the incorrect type=MAQMapview, pattern > ambiguity seemed not to be an issue. I'd expect to see the ambiguity > error in both MAQMap and MAQMapview cases. yes and this is also the reason for the poor error message -- MQAMap differs from most input functions in that it really expects just a single file for input; MAQMapview would have happily read in (to a single AlignedRead object) all files matching the pattern. I'll try to improve the error message (in the development branch). Martin > G > > On 4/30/09 11:16 AM, "Martin Morgan" <[email protected]> wrote: > > Hi Gordon -- > > Gordon Robertson wrote: > > I'm starting to learn to use ShortRead, so apologize if I've missed > > something simple. I've read the relevant sections of the three PDF > docs that > > are available from the ShortRead web page. > > > > I'm using R-2.9.0, compiled from source on 64-bit RehHat > Enterprise Linux, > > and installed ShortRead within the past two weeks. > > > > Briefly, I'm able to load an Illumina Export file, but not the > corresponding > > Maq file. I don't understand the MAQmap error message, but I don't > get such > > an error when I change the dirPath, pattern and type and rerun to > load the > > SolexaExport file, which is in the folder above the 'map' file. > And I seem > > to be able to start to load the 'map' file using an incorrect > 'MAQMapview' > > type. > > > > 1. Attempt to read a MAQ 0.7.1 'map' file > > > readAligned("/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq/", > > pattern="30WLMAAXX_5.map", type="MAQMap") > > Error: UserArgumentMismatch > > 'dirPath', 'pattern' must be 'character(1)' > > I think the problem is that your 'pattern' isn't specific enough, e.g., > > list.files("/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq/", > pattern="30WLMAAXX_5.map") > > matches more than one file; often "^30WLMAAXX_5.map$" is more > appropriate. > > Martin > > > > > 2. Try the Illumina 'export' file > > > readAligned("/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/", > > pattern="30WLMAAXX_5_export.txt", type="SolexaExport") > > class: AlignedRead > > length: 15256798 reads; width: 76 cycles > > chromosome: QC QC ... QC QC > > position: NA NA ... NA NA > > strand: NA NA ... NA NA > > alignQuality: NumericQuality > > alignData varLabels: run lane ... y filtering > > > > 3. As a test, I can apparently start to load the 'map' file using > > type=MAQMapview. > > > readAligned('/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq/', > > pattern='30WLMAAXX_5.map', type='MAQMapview') > > Error: Input/Output > > 'readAligned' failed to parse files > > dirPath: '/archive/solexa1_4/analysis/HS1035/30WLMAAXX_5/maq/' > > pattern: '30WLMAAXX_5.map' > > type: 'MAQMapview' > > error: scan() expected 'an integer', got > > > 'vv####################]}################?##Mq###7,##^|D#####X~!D######' > > > > -- > > Could you help me understand why I'm unable to readAligned the > 'map' file? > > Again, I apologize if I've missed something simple. Thanks for > your help. > > > > G > > > -- > 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 > > > > -- > Gordon Robertson > Gene Regulation Informatics > Canada's Michael Smith Genome Sciences Centre > Vancouver BC Canada > www.bcgsc.ca > -- 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 -- Gordon Robertson Gene Regulation Informatics Canada's Michael Smith Genome Sciences Centre Vancouver BC Canada www.bcgsc.ca [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
