# R code Chapter 21 text manipilation part 1

tr1<-"(((((BBTH004_16_CCDB_24026_A4_91Tachinidae[90Drosophila]:1.14675336480776657311,(BBTH006_16_CCDB_24026_A6_91Belvosia:0.59297714057027572920,BBTH055_16_CCDB_24026_E7_92Tachinidae[91Belvosia]:0.52736765819178677006):0.32998852276617751667):0.31714205003432383023,((BBTH084_16_CCDB_24026_G12_97Tachinidae:0.00006954085997979414,BBTH085_16_CCDB_24026_H1_97Tachinidae:0.00006954085997979414):0.00006954085997979414,(BBTH080_16_CCDB_24026_G8_97Tachinidae:0.00006954085997979414,BBTH091_16_CCDB_24026_H7_97Tachinidae:0.00006954085997979414)"
tr2<-gsub("16_CCDB_24026_","",tr1)
# tr2
tr3<- gsub("BBTH.+?24026", "BBTH24026", tr1)
# tr3
tr4<- gsub("\\[.+?\\]", "", tr3) #this means remove everything between [ and ]
# tr4
tr5<- strsplit(tr4,"")
tr5<-unlist(tr5)
# head(tr5,40)
colon<-which(tr5==":")
colon
close<-which(tr5==")")
comma<-which(tr5==",")
# close
# comma
tr5[colon[1]:(comma[1]-1)] 

# Method 1
tr4<- gsub("\\[.+?\\]", "", tr3)
repeat{
ss<-unlist(strsplit(tr4, ""))
colon<-which(ss==":") 
L<-length(unlist(colon)) 
if(L==0)break
close<-which(ss==")") 
comma<-which(ss==",") 
a<-which(comma>colon[1])
b<-which(close>colon[1])
c<-min(comma[a[1]],close[b[1]]) 
n<-substr(tr4,colon[1],c-1) 
tr4<-gsub(n,"",tr4) 
}
tr4

# Method 2
tr4<- gsub("\\[.+?\\]","",tr3)
tr5<- unlist(strsplit(tr4,""))
colons<-grep(":",tr5)
ends<-colons+22 
for(i in length(colons):1) tr4<-gsub(substr(tr4,colons[10],ends[10]),"",tr4)
tr4

# Method 3
tr4<-gsub("\\[.+?\\]","",tr3)
tr5<-unlist(strsplit(tr4,""))
colons<-grep(":",tr5)
ends<-colons+22 # 22 including the colon
positions<-NULL
for(i in 1:length(colons)){
temp<-colons[i]:ends[i]
positions<-c(positions,temp)}
tr5<-tr5[-positions]
tr4<-paste(tr5,collapse="")
tr4 

# Extracting names and well number
names<-gsub("\\(","",tr4)
names<-unlist(strsplit(names,")"))
names<-unlist(strsplit(names,","))
# names
names<-names[which(names!= "")]
names

# rearranging names
rearrange<-NULL
for(i in 1:length(names)){
temp<-unlist(strsplit(names[i],"_")) 
# temp = "BBTH24026"    "A4"     "91Tachinidae"
rearrange<-c(rearrange,paste(temp[2],temp[1],temp[3],sep="_")) 
}
rearrange
sort(rearrange)