Nothing
compare <- function(ctFile1,ctFile2){
RNAstructure1 <- ctFile1
RNAstructure2 <- ctFile2
hairpin_loop_1 <- unlist(hairpin_loop(RNAstructure1))
hairpin_loop_2 <- unlist(hairpin_loop(RNAstructure2))
internal_loop_1 <- unlist(internal_loop(RNAstructure1))
internal_loop_2 <- unlist(internal_loop(RNAstructure2))
bulge_loop_1 <- unlist(bulge_loop(RNAstructure1))
bulge_loop_2 <- unlist(bulge_loop(RNAstructure2))
multi_branch_loop_1 <- unlist(multi_branch_loop(RNAstructure1))
multi_branch_loop_2 <- unlist(multi_branch_loop(RNAstructure2))
stem_1 <- unlist(stem(RNAstructure1))
stem_2 <- unlist(stem(RNAstructure2))
if(length(union(stem_1,stem_2)) == 0){
score_1 <- 1
}else{
score_1 <-length(intersect(stem_1,stem_2))/length(union(stem_1,stem_2))
}
if(length(union(multi_branch_loop_1,multi_branch_loop_2)) == 0){
score_2 <- 1
}else{
score_2 <-length(intersect(multi_branch_loop_1,multi_branch_loop_2))/length(union(multi_branch_loop_1,multi_branch_loop_2))
}
if(length(union(bulge_loop_1,bulge_loop_2)) == 0){
score_3 <- 1
}else{
score_3 <-length(intersect(bulge_loop_1,bulge_loop_2))/length(union(bulge_loop_1,bulge_loop_2))
}
if(length(union(internal_loop_1,internal_loop_2)) == 0){
score_4 <- 1
}else{
score_4 <-length(intersect(internal_loop_1,internal_loop_2))/length(union(internal_loop_1,internal_loop_2))
}
if(length(union(hairpin_loop_1,hairpin_loop_2)) == 0){
score_5 <- 1
}else{
score_5 <-length(intersect(hairpin_loop_1,hairpin_loop_2))/length(union(hairpin_loop_1,hairpin_loop_2))
}
if(max(length(stem_1),length(stem_2)) == 0){
score_6 <- 1
}else{
score_6 <- min(length(stem_1),length(stem_2))/max(length(stem_1),length(stem_2))
}
if(max(length(multi_branch_loop_1),length(multi_branch_loop_2)) == 0){
score_7 <- 1
}else{
score_7 <- min(length(multi_branch_loop_1),length(multi_branch_loop_2))/max(length(multi_branch_loop_1),length(multi_branch_loop_2))
}
if(max(length(bulge_loop_1),length(bulge_loop_2)) == 0){
score_8 <- 1
}else{
score_8 <- min(length(bulge_loop_1),length(bulge_loop_2))/max(length(bulge_loop_1),length(bulge_loop_2))
}
if(max(length(internal_loop_1),length(internal_loop_2)) == 0){
score_9 <- 1
}else{
score_9 <- min(length(internal_loop_1),length(internal_loop_2))/max(length(internal_loop_1),length(internal_loop_2))
}
if(max(length(hairpin_loop_1),length(hairpin_loop_2)) == 0){
score_10 <- 1
}else{
score_10 <- min(length(hairpin_loop_1),length(hairpin_loop_2))/max(length(hairpin_loop_1),length(hairpin_loop_2))
}
score <- score_1 + score_2 + score_3 + score_4 + score_5 + score_6 + score_7 + score_8 + score_9 + score_10
return(score)
}
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