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