[BioC] how to read empty line in the fastqfile

[Martin Morgan]

On 03/08/2012 01:59 PM, wang peter wrote:
> i often meet this problem after trimming the adapters
>
>
>> reads<- readFastq(fastqfile);
> Error: Input/Output
>    file(s):
>      L003GAF-128.trimmed
>    message: unexpected empty line L003GAF-128.trimmed:61

Reading zero-length records has been enabled in the devel version 
ShortRead 1.13.16; use the devel version of R and install ShortRead via

   source('http://bioconductor.org/biocLite.R')
   biocLite('ShortRead')

As Steve suggests, filtering on the way out might be sensible  -- 
fq[width(fq) != 0].

Martin

>
> R version 2.14.1 (2011-12-22)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ShortRead_1.12.4    latticeExtra_0.6-19 RColorBrewer_1.0-5
> [4] Rsamtools_1.6.3     lattice_0.20-0      Biostrings_2.22.0
> [7] GenomicRanges_1.6.7 IRanges_1.12.6
>
> loaded via a namespace (and not attached):
>   [1] Biobase_2.14.0     bitops_1.0-4.1     BSgenome_1.22.0    grid_2.14.1
>   [5] hwriter_1.3        RCurl_1.91-1       rtracklayer_1.14.4 tools_2.14.1
>   [9] XML_3.9-4          zlibbioc_1.0.0
>
>


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