[BioC] how to read empty line in the fastqfile

[Martin Morgan]

On 03/08/2012 03:45 PM, Martin Morgan wrote:
> 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

I meant to say the 2.15 alpha version of R.

>
> 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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