[R] Convert CSV file to FASTA

[Martin Morgan]

On 08/31/2011 01:36 AM, anyone wrote:
> Hi there,
>
> I have large excel files which I can save as CSV files.
>
> Each excel file contains two columns. One contains the chromosome number and
> the second contains a DNA sequence.
>
> I need to convert this into a fasta file that looks like this
>> chromosomenumber
> CGTCGAGCGTCGAGCGGAGCG....
>
> Can anyone show me an R script to do this?

Hi x

along the lines of

   csv = read.csv("foo.csv")
   fa = character(2 * nrow(csv))
   fa[c(TRUE, FALSE)] = sprintf("> %s", csv$chr)
   fa[c(FALSE, TRUE)] = csv$seq
   writeLines(fa, "foo.fasta")

perhaps use scan() instead of read.csv if your input file is simple enough.

The Bioconductor project has many packages for dealing with sequence 
data, including Biostrings and ShortRead; both would enable this, e.g.,

    ## once only
    source("http://bioconductor.org/biocLite.R")
    biocLite("Biostrings")

    ## then...
    library(Biostrings)
    seq = csv$seq
    names(seq) = csv$id
    dna = DNAStringSet(seq)
    write.XStringSet(dna, "foo.fasta")

which would be worth the effort if you wanted to use R for more than an 
awk replacement.

Martin

>
> Many thanks
>
> x
>
> --
> View this message in context: http://r.789695.n4.nabble.com/Convert-CSV-file-to-FASTA-tp3780498p3780498.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793