[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 This has been superseded by readDNAStringSet(), writeXStringSet(), etc...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
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