## runSNPMaP.R
## Copyright (c) 2008 Oliver SP Davis and Leo Schalkwyk

## This file is part of the SNPMaP package.

## SNPMaP is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.

## SNPMaP is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
## GNU General Public License for more details.

## You should have received a copy of the GNU General Public License
## along with SNPMaP.  If not, see <http://www.gnu.org/licenses/>.

## Usage:
## R --no-save <runSNPMaP.R
##
## This should process the arrays in the same directory as the script
## Alternatively, if .R file extension is associated with R or with the Rscript
## executable (eg. via 'Properties' in Windows), then you should be able to
## double-click the script icon

## Start a log file
logf<-file('SNPMaP_log.log', 'w')
sink(logf, split=TRUE)
sink(logf, type='message')
cat('runSNPMaP.R\n')
cat(date(), '\n')

## Load SNPMaP library (try to install if necessary)
if(!require(SNPMaP)){
	install.packages('SNPMaP')
	library(SNPMaP)
}

## Read in arrays (interactive file choice on Windows)
if(.Platform$OS.type == "windows"){
	snps<-msnpmap(interactive=TRUE)
}else{
	snps<-msnpmap()
}

## Set up some file names for the output
mats<-names(snps)
chp<-getSNPMaP(snps[[1]], 'chiptype')
files<-paste(chp, '_', mats, '.csv', sep='')

## Write the SNPMaP matrices to comma-separated files
cat('Writing files ...\n')
for(i in 1:length(files)){
	writeSNPMaP(snps[[i]], file=files[i], sep=",", transpose=FALSE)
}
cat('Done(SNPMaP).\n')
cat(date(), '\n')

## Tidy up
rm(mats, chp, files, i)
sink()
sink(type='message')
flush(logf)
close(logf)

## Save the environment
save.image('SNPMaP_env.RData')