[BioC] CharacerToFASTArecords

Nair, Murlidharan T mnair at iusb.edu
Sat Feb 16 02:45:25 CET 2013


Hervé, 

I thought CharacterToFASTArecords() would convert it to the format when I read data using  read.fasta from bio3d package. Since I am getting the data after querying a database so I get it as a string. Is there a method that will covert it into an object returned by readDNAStringSet(). 

Thanks ../Murli


-----Original Message-----
From: Hervé Pagès [mailto:hpages at fhcrc.org] 
Sent: Friday, February 15, 2013 6:47 PM
To: Murli [guest]
Cc: bioconductor at r-project.org; Nair, Murlidharan T
Subject: Re: CharacerToFASTArecords

Hi Murli,

On 02/15/2013 11:22 AM, Murli [guest] wrote:
> Hi,
>
> Is there any other method in Biostrings_2.26.3 that does what CharacterToFASTArecords does in Biostrings_2.16.9? Or do I need to install the old version and use the method from it?

Here is how the function was defined:

   CharacterToFASTArecords <- function(x)
   {
     if (!is.character(x))
         stop("'x' must be a character vector")
     lapply(seq_len(length(x)),
            function(i) list(desc=names(x)[i], seq=x[[i]]))
   }

I would just put it in my script or package if I was you. Or even better, I would update my code to make use of the native DNAStringSet/AAStringSet functionalities. CharacterToFASTArecords() is from the old times when DNA (or AA) sequences were stored as an ordinary list after loading them with readFASTA() or before sending them to a file with writeFASTA(). This has been superseded by readDNAStringSet(), writeXStringSet(), etc... for at least 3 years and I cannot think of any good reason for storing sequences in an ordinary list in 2013.

Cheers,
H.

>
> Cheers../Murli
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.2 (2012-10-26)
> 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] Biostrings_2.26.3  IRanges_1.16.4     BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> [1] parallel_2.15.2 stats4_2.15.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319



More information about the Bioconductor mailing list