## ExerciseBox_24.1_reverse_comp

# preliminary, generate upper and lower case sequences
randomDNAup<-paste(sample(c("A","C","G","T"),100,rep=TRUE,prob=c(0.25,0.25,0.25,0.25)),collapse="")
randomDNAlow<-paste(sample(c("a","c","g","t"),100,rep=TRUE,prob=c(0.25,0.25,0.25,0.25)),collapse="")


#  Part 1
s<-randomDNAup
#OR
s<-randomDNAlow


# test if upper case
ifelse(s==toupper(s),is.upper<-TRUE,is.upper<-FALSE)
is.upper


library(seqinr)
reverse_complement<-paste(rev(comp(unlist(strsplit(s,"")))),collapse="")
if(is.upper) reverse_complement<-toupper(reverse_complement)
#reverse_complement


#  Part 2
# preliminary, generate upper and lower casesequences
randomDNAwithXs<-paste(sample(c("A","C","G","T","N","X"),100,rep=TRUE,prob=c(0.23,0.23,0.23,0.23,.02,.04)),collapse="")
# randomDNAwithXs 

s<-unlist(strsplit(randomDNAwithXs,""))
map=c("A"="T","T"="A","G"="C","C"="G","N"="N","X"="X","t"="a","a"="t","c"="g","g"="c","n"="n","x"="x")
revcompDNAwithNX<- paste(rev(map[s]),collapse="")
revcompDNAwithNX