Hello guest with no name,

Have you tried something simple?

library(ShortRead)
mysequences <- readFasta('FileName.fa')

Cheers,

Ivan



Ivan Gregoretti, PhD
Bioinformatics



On Fri, Mar 28, 2014 at 12:56 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 03/28/2014 09:43 AM, DNAStringSet Error Biostrings in R [guest] wrote:
>
>>
>> I posted this same quandary on Biostars and stack overflow.
>>
>> I am attempting to import a fasta file of sequences into R using
>> Bioconductor's 'Biostrings' package and the 'DNAStringSet' function but I
>> keep getting the same error:
>>
>> Error in .Call2("new_XString_from_CHARACTER", classname, x,
>> start(solved_SEW),  :
>> key 112 (char 'p') not in lookup table
>>
>> My fasta file ("FileName.fa") is comprised of various length sequences,
>> in the following format:
>>
>>  GeneNameOne
>>>
>> CAGACACCCATAGATACAGATAGACAGATAGAGAAGACACCACCACACAATGA
>>
>>> GeneNameTwo
>>>
>> CGCGACATGAACCCATGATAGACGATGAGACCCCACACACACC
>> ...etc
>>
>> I performed 'grep p FileName.fa' in the Unix terminal, but I received no
>> output.
>>
>
> you could try a divide-and-conquer approach, splitting the file into two
> and read each and choose the half with a problem and continue. Please
> continue reading below...
>
>
>
>> Does anyone have an idea on what is going on?
>>
>> Thanks in advance.
>>
>>   -- output of sessionInfo():
>>
>> Error in .Call2("new_XString_from_CHARACTER", classname, x,
>> start(solved_SEW),  :
>> key 112 (char 'p') not in lookup table
>>
>
> Rather than repeating the error without context, it is usually helpful to
> cut-and-paste the relevant portions of the session that causes problems,
> e.g.,
>
> > library(Biostrings)
> > readLines("FileName.fa", 4)   ## correct file?
> [1] "> GeneNameOne"
> [2] "CAGACACCCATAGATACAGATAGACAGATAGAGAAGACACCACCACACAATGA"
> [3] "> GeneNameTwo"
> [4] "CGCGACATGAACCCATGATAGACGATGAGACCCCACACACACC"
> > readDNAStringSet("FileName.fa")
>
> Error in .Call2("new_XString_from_CHARACTER", classname, x,
> start(solved_SEW), : key 112 (char 'p') not in lookup table
>
> The information being asked for here is the output of the command
> sessionInfo() so that basic information about your system is available;
> here's mine,
>
> > library(Biostrings)
> > sessionInfo()
> R version 3.0.2 Patched (2014-01-02 r64626)
> Platform: x86_64-unknown-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=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] Biostrings_2.30.1  XVector_0.2.0      IRanges_1.20.6
> BiocGenerics_0.8.0
>
> loaded via a namespace (and not attached):
> [1] stats4_3.0.2
>
>
>
>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>>
>
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