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stepwise.seqs<-function(file, remGaps=TRUE) {
info<-scan(file, n=2, quiet=TRUE)
numseqs<-info[1]; seqlength<-info[2]
chStrings<-scan(file,what=character(),sep="\n", quiet=TRUE)
#read each row of file into a character string
chStrings<-chStrings[-1] #don't need first row
seqNames<-rep(NA,numseqs)
dat<-matrix(NA,nrow=numseqs,ncol=seqlength)
for(i in 1:numseqs) {
seqNames[i]<-substring(chStrings[i],first=1,last=10)
dat[i,]<-substring(chStrings[i],first=(11:(10+seqlength)),
last=(11:(10+seqlength)))
}
colnames<-paste("s",(1:seqlength),sep="")
dimnames(dat)<-list(seqNames,colnames)
if(remGaps) {
indmat<-dat=="-"
chuckcol<-apply(indmat,2,any)
dat<-dat[,!chuckcol]
}
return(dat)
}
stepwise.seqs<-stepwise.seqs("simulinfile.txt")
save(stepwise.seqs,file="stepwise.seqs.RData")
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