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. Help appreciated. Thanks -- Fahim Mohammad CECS, univ of Louisville [[alternative HTML version deleted]]

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

Quoting Fahim Md <fahim.md at="" gmail.com="">: > 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. > > Help appreciated. Thanks I don't think there's a package that does that, but you can call the program from R using system(). I was looking for an example where I did just that, and I found another alternative that may not be the most elegant but I can confirm it worked: IN this case I run the netblast program, which I downloaded and was located in my working directory. 1) construct command line, where 'file' was the name of the file containing fasta sequences, and 'outfile' the name of the desired output file: line<-paste("blastcl3.exe -p blastn -d nr -i ",file," -o ",outfile," -m 8 -u Homo[organism] -v 1 -b 1",sep="") 2) run it: scan(pipe(line)) 3) read blast output: readoutput<-read.table(outfile, sep="\t", as.is=T) Not sure why I used the scan & pipe route (this was done a while ago, I tend to use Perl for anything dealing with file formatting and running external programs), I'd have imagined all you need was a call to system(). I hope it helps a bit... Jose -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6507095 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK ********************************************* Alternative email: nach.mcnach at gmail.com ********************************************* -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.