[BioC] using Blat in R

[Sean Davis]

On Sun, Apr 11, 2010 at 11:45 AM, Fahim Md <fahim.md at gmail.com> wrote:
> I am trying to use "blat-blast like alignment tool" in R. I couldn't find
> any package in CRAN or bioconductor. I downloaded the windows executable
> from Jim Kent's (from ucsc) webpage. I am wondering how to use/call these
> functions embedded in these executables. I have some results in R that would
> be input to these executable file and then store and process the output of
> these executable file in R.
>
>  I am seeking for some direction or some material that addresses such
> problem. I am considering "system()" but I am nor sure how far can I go with
> this.

Hi, Fahim.

I do not think that blat functionality is available directly from R.
The idea, then is to:

1) write the data from R to a fasta file
2) use system() to run blat (or just run blat from the command line)
3) read the results back into R from the resulting blat output file

There isn't anything else tricky, I don't think.

Sean