[Bioc-sig-seq] ShortRead qa() no longer working

[Martin Morgan]

  Hi Dario --

On 8/25/2010 12:00 AM, Dario Strbenac wrote:
> Hello,
>
> I've updated my ShortRead and IRanges packages recently and the qa function doesn't

I'm guessing that you mean you updated from ShortRead 1.6.0. to 1.6.2. 
There don't look like there are code changes that would cause problems 
with this...

> work for me anymore. It spends a couple of minutes processing, then fails with an error :
>
>> str(path)
> chr "C:/Users/dario/Documents/Garvan/rawData/seq/Ramaciotti/25-03-2010/s_1_1"
>
>> dir(path)
> [1] "12627LN-FFPET_MBD2IP_1.Rdata"    "12627LN-FFPET_MBD2IP_1.wig.gz"   "12627LN-FFPET_MBD2IP_1_GR.Rdata" "mapping.log"                     "s_1_sequence.fastq.gz"           "s_1_sequence.uniq.map.gz"
>
>> QAfastq<- qa(path, "fastq.gz", "fastq")
> Error in stop(msg, " ", errors, domain = NA) :
>    no function to return from, jumping to top level
> Error in slot(object, ".srlist") :
>    cannot get a slot (".srlist") from an object of type "NULL"
> In addition: Warning message:
> UnspecifiedWarning
>    elements: 1
>    UnspecifiedError: qa(readFastq(dirPath, pattern, ...), pattern, verbose = verbose)
>   error in evaluating the argument 'dirPath' in selecting a method for function 'qa'

does

    fl = list.files(path, "fastq.gz", full=TRUE)

return something sensible (just the path to s_1_seqeunce.fastq.gz)?

Does

   .Call(ShortRead:::.read_solexa_fastq, fl, TRUE)

return a list containing the sequences, ids, and qualities? If not, then 
there are problems parsing the fastq file. The parser expects the reads 
/ qualities to occupy a single line each, and the qualities to be 
encoded. Is that the case for these reads? Also, how many and what 
length are the reads supposed to be?

Martin
>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> x86_64-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                       LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.6.2     Rsamtools_1.0.0     lattice_0.18-5      Biostrings_2.16.0   GenomicRanges_1.0.7 IRanges_1.6.15
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 grid_2.11.0   hwriter_1.2   tools_2.11.0
>
> Could this be a bug in the function ?
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
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