# --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# Copyright (C) 2007 Author: Martha Nason

# This program 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 2 of the License, or any later version.

# This program 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 this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
# ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

#This is a function to create files of sets of genes where the lengths are specified as a vector (m) 
#	and the probabilities of each letter is given by pA, pC, pT, or pG

Gene.cluster.null <- function(m,nGenes=length(m),pACTG,length=max(m), filename="c:\\searchpattool\\sampletest.txt"){
	temp <- matrix(" ",nrow=nGenes,ncol=length)

	for (i in 1:nGenes) {
		write(paste(">seq",i,sep=""),file=filename,append=i!=1)
if (is.vector(pACTG)){
			temp[i,1:m[i]] <- sample(rep(c("A","C","T","G"),times=rmultinom(1,m[i],pACTG)))}
else if (is.matrix(pACTG)){
			print("UNDER CONSTRUCTION-- use vector of probabilities for now"); break
			}
		write.table(temp[i,], file = filename, append = TRUE, quote = FALSE, sep = "",
                 eol = "", na = "NA", dec = ".", row.names = FALSE,
                 col.names = FALSE, qmethod = c("escape", "double"))
		write("",file=filename,append=TRUE)
	}
}


# Example Call
#Gene.cluster.null(m=c(10,8,6,5,12),pACTG=c(.4,.1,.3,.2))



#This function allows you to loop a specified number of times (1000) 
#  and call the above function, creating separate files for each call.

Create.multiple.Files<- function(nFiles=1000,m, pACTG,filename.root){
	for (j in 1:nFiles){
		Gene.cluster.null(m=m,pACTG=pACTG,filename=paste(filename.root,j,".txt",sep=""))
	}
	
}

#Examples Call
#1
Create.multiple.Files(3,m=c(10,8,6,5,12),pACTG=c(.4,.1,.3,.2),filename.root="C:\\searchpattool\\sample")

#create 3 random files: sample1.txt, sample2.txt and sample3.txt. Each file has 5 sequences with the background probabilties 0.4, 0.1, 0.3 and 0.2. The length of the sequences are 
# respectively 10, 8, 6 ,5 and 12

#2
Create.multiple.Files(1000,m=c(197,264,195,218,206,451,332,245,245,448,230,451,434,241,172,267,171,207,451,451,161),pACTG=c(.328008,.167476,.193845,.310671),filename.root="C:\\searchpattool\\sample")

#create 1000 random files: sample1.txt, sample2.txt ....and sample1000.txt. Each file has 21 sequences with the background probabilties 0.328008,0.167476,0.193845 and 0.310671. The length
# of the sequences are respectively 197,264,195,218,206,451,332,245,245,448,230,451,434,241,172,267,171,207,451,451 and 161.