Thanks, that work. That is what I was looking for. Cheers../Murli -----Original Message----- From: Hervé Pagès [mailto:hpages@fhcrc.org] Sent: Tuesday, February 19, 2013 2:59 PM To: Nair, Murlidharan T Cc: Murli [guest]; bioconductor at r-project.org Subject: Re: CharacerToFASTArecords Hi Murli, On 02/15/2013 05:45 PM, Nair, Murlidharan T wrote: > Herv?, > > 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(). The object returned by readDNAStringSet() is DNAStringSet. So if your question is "is there a method to convert the string I get from the database into a DNAStringSet object?", then the answer is "yes, just pass it to the DNAStringSet() constuctor". Cheers, H. > > 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 This has been superseded by readDNAStringSet(), writeXStringSet(), etc...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 > -- 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