p<-unlist(strsplit("ATCTCGGCGCGCATCGCGTACGCTACTAGC",""))
p
map=c("A"="T", "T"="A","G"="C","C"="G")
map[p]
unname(map[p])
sapply(p, switch,  "A"="T", "T"="A","G"="C","C"="G")
RCOMP<-function(x){
r<-sapply(lapply(strsplit(x, NULL), rev), paste, collapse="") 
y<-paste(map[unlist(strsplit(r, NULL))],collapse="")
return(y) 
}

# install.packages("seqinr")
library(seqinr)
comp()
comp(p)
rev(comp())

c2s(comp(s2c("AAAATTTTGGGGCCCC")))
c2s(rev(comp(s2c("aaaattttggggcccc"))))
allbases <- s2c("atgcmynnsk")
comp(allbases)
comp(allbases, ambiguous = TRUE)

#####

install.packages("BiocManager")
library(Biostrings)
dna=DNAStringSet(c("ATCTCGGCGCGCATCGCGTACGCTACTAGC","ACCGCTA"))
complement(dna)


#####

rnasq<-"UAUAUUUCAAAUAUAAAGUAAUUUAGAAAGUAAGAUCAAAGAUUAAU"
types<-"PPPPPUUUUPPPPPPPUPPUUUPPPPUUUUUUUUUUPPPPPPUUUUU"
U<-which(unlist(strsplit(types,""))=="U")
P<-which(unlist(strsplit(types,""))=="P")
Pgroups<-split(P,cumsum(c(1,diff(P) != 1)))
# c(1,diff(P))
# c(1,diff(P) !=1)
# cumsum(c(1,diff(P) != 1))


######
randomDNA<-paste(sample(c("A","C","G","T"),10000,rep=TRUE,prob=c(0.4,0.1,0.1,0.4)), collapse="")

######
# install.packages("ape") 
library(ape) 
Monilobracon1<-read.GenBank("AY529648",as.character=TRUE)
# Monilobracon1
# mode(Monilobracon1)
# str(Monilobracon1)
# Monilobracon1$AY529648[1:80]
s<-paste(Monilobracon1$AY529648,collapse="")
# s
attributes(Monilobracon1)[1]
attributes(Monilobracon1)[2]


all_Monilos<-c("MH234998","MH260676","AY296646","AY529647","AY532320", "AY529649","AJ296046")
Mons<-read.GenBank(all_Monilos,as.character=TRUE)
data<-cbind(attr(Mons,"species"),names(Mons))
# data
write.dna(Mons,file="Monilobracon.fas",format="fasta",nbcol=6,colsep=" ",colw=10)

######
Xenarcha<-"000000010000001011101111000000000?01?100001000?0?0100"
Colastes<-"000000010000011001101011000000000?01?110101000?0?0100"
Gnamptodon<-"000000010000001001001001001000111?01?0?0001?00?0?0101"
wasps<-rbind(Xenarcha,Colastes,Gnamptodon)
# wasps
newwasps<-wasps
for(i in 1:length(wasps)){
	newdata<-NULL
	for(j in 1:nchar(wasps[i])){
    ifelse(is.whole(j/5),newdata<-paste(newdata,substr(wasps[i],j,j), "",collapse="",sep=""),newdata<-paste(newdata,substr(wasps[i],j,j), collapse="",sep=""))
    }
if(i==1) ONE<-TRUE
	if(i==2) TWO<-TRUE
newwasps[i]<-newdata}
newwasps

######
names<-NULL
for(i in 1:length(tuatara)) names<-c(names,unlist(strsplit(tuatara[i]," "))[1])
# names
names<-unlist(lapply(strsplit(tuatara,split=" "),"[",1))
# names
tuatara[6]<-gsub("*\\(.*?\\)","?", tuatara[6])