[Bioc-sig-seq] Problem loading MAQ map file in ShortRead

[Martin Morgan]

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" <mtmorgan at fhcrc.org> 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