//After identifying the exons and introns of an RNA string, we only need to delete the introns and concatenate the exons to form a new string ready for translation.
//
//Given: A DNA string s (of length at most 1 kbp) and a collection of substrings of s acting as introns. All strings are given in FASTA format.
//
//Return: A protein string resulting from transcribing and translating the exons of s. (Note: Only one solution will exist for the dataset provided.)
//
//Sample Dataset
//
//>Rosalind_10
//ATGGTCTACATAGCTGACAAACAGCACGTAGCAATCGGTCGAATCTCGAGAGGCATATGGTCACATGATCGGTCGAGCGTGTTTCAAAGTTTGCGCCTAG
//>Rosalind_12
//ATCGGTCGAA
//>Rosalind_15
//ATCGGTCGAGCGTGT
//Sample Output
//
//MVYIADKQHVASREAYGHMFKVCA
func SpliceRna(filename string) (protein string) {
dna, introns, err := readSplcInput(filename)
if err != nil {
panic("failed to read input from " + filename)
}
st := suffix_tree.ConstructSuffixTree(dna)
intronOffsets := make(map[int]int)
for _, intron := range introns {
for pos := range suffix_tree.FindSubstrings(st, intron) {
intronOffsets[pos] = len(intron)
}
}
exons := make([]rune, len(dna))
intronEnd := 0
inIntron := false
l := 0
for i, r := range dna {
if length, present := intronOffsets[i]; present && i+length >= intronEnd {
intronEnd = length + i
inIntron = true
}
if i >= intronEnd {
inIntron = false
}
if !inIntron {
exons[l] = r
l++
}
}
// fmt.Printf("dna : %v\n", string(dna))
// fmt.Printf("exons: %v\n", string(exons))
retVal := EncodeProtein(TranscribeRna(string(exons)))
// fmt.Printf("retVal: %v\n", string(retVal))
return retVal
}
func RnaSplice(input string) (protein string) {
var lineBreaks []int
for i, r := range input {
if r == '\n' {
lineBreaks = util.AppendInt(lineBreaks, i)
}
}
dna := input[lineBreaks[0]+1 : lineBreaks[1]]
// fmt.Println(dna)
st := suffix_tree.ConstructSuffixTree(dna)
intronOffsets := make(map[int]int)
intronStart := lineBreaks[1] + 1
for i, lineBreak := range lineBreaks[2:] {
if i%2 == 1 {
// fmt.Println(input[intronStart:lineBreak])
// fmt.Println(suffix_tree.FindSubstrings(st, input[intronStart:lineBreak]))
for k, _ := range suffix_tree.FindSubstrings(st, input[intronStart:lineBreak]) {
// intronOffsets = util.AppendInt(intronOffsets, k)
intronOffsets[k] = lineBreak - intronStart
}
//fmt.Printf("intronOffsets: %v\n", intronOffsets)
}
intronStart = lineBreak + 1
}
exons := make([]rune, len(dna))
intronEnd := 0
inIntron := false
l := 0
for i, r := range dna {
if length, present := intronOffsets[i]; present && i+length >= intronEnd {
//intronEnd = intronOffsets[i]
intronEnd = length + i
//fmt.Printf("in new intron: %v\n", intronEnd)
inIntron = true
}
if i >= intronEnd {
inIntron = false
}
if !inIntron {
exons[l] = r
l++
}
}
//fmt.Printf("dna : %v\n", string(dna))
//fmt.Printf("exons: %v\n", string(exons))
//return TranscribeRna(string(exons))
retVal := EncodeProtein(TranscribeRna(string(exons)))
// fmt.Printf("retVal: %v\n", string(retVal))
return retVal
// return input
}