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/*
* kmer.cpp
*
*
* Created by Pat Schloss on 12/15/08.
* Copyright 2008 Patrick D. Schloss. All rights reserved.
*
*/
#include "kmer.hpp"
/**************************************************************************************************/
Kmer::Kmer(int size) : kmerSize(size) { // The constructor sets the size of the kmer
int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
// No reason to waste the time of recalculating
maxKmer = power4s[kmerSize]+1;// (int)pow(4.,k)+1; // powers of 4 everytime through. We need an
// extra kmer if we get a non-ATGCU base
}
/**************************************************************************************************/
string Kmer::getKmerString(string sequence){ // Calculate kmer for each position in the sequence, count the freq
int length = sequence.length(); // of each kmer, and convert it to an ascii character with base '!'.
int nKmers = length - kmerSize + 1; // Export the string of characters as a string
vector<int> counts(maxKmer, 0);
for(int i=0;i<nKmers;i++){ // Go though sequence and get the number between 0 and maxKmer for that
int kmerNumber = getKmerNumber(sequence, i);// kmer. Increase the count for the kmer in the counts vector
counts[kmerNumber]++;
}
string kmerString = "";
for(int i=0;i<maxKmer;i++){ // Scan through the vector of counts and convert each element of the
kmerString += getASCII(counts[i]); // vector to an ascii character that is equal to or greater than '!'
}
return kmerString;
}
/**************************************************************************************************/
vector< map<int, int> > Kmer::getKmerCounts(string sequence){ // Calculate kmer for each position in the sequence, save info in a map
int length = sequence.length(); // so you know at each spot in the sequence what kmers were found
int nKmers = length - kmerSize + 1; //
vector< map<int, int> > counts; counts.resize(nKmers); // a map kmer counts for each spot
map<int, int>::iterator it;
for(int i=0;i<nKmers;i++){ // Go though sequence and get the number between 0 and maxKmer for that
if (i == 0) {
int kmerNumber = getKmerNumber(sequence, i);// kmer.
counts[i][kmerNumber] = 1; // add this kmer if not already there
}else {
//your count is everything that came before and whatever you find now
counts[i] = counts[i-1];
int kmerNumber = getKmerNumber(sequence, i);// kmer.
it = counts[i].find(kmerNumber);
if (it!= counts[i].end()) { counts[i][kmerNumber]++; } //increment number of times you have seen this kmer
else { counts[i][kmerNumber] = 1; } // add this kmer since not already there
}
}
return counts;
}
/**************************************************************************************************/
int Kmer::getKmerNumber(string sequence, int index){
// Here we convert a kmer to a number between 0 and maxKmer. For example, AAAA would equal 0 and TTTT would equal 255.
// If there's an N in the kmer, it is set to 256 (if we are looking at 4mers). The largest we can look at are 8mers,
// this could be easily increased.
//
// Example: ATGCAT (kSize = 6)
// i: 012345
//
// Score = 0*4^(6-0-1) + 3*4^(6-1-1) + 2*4^(6-2-1) + 1*4^(6-3-1) + 0*4^(6-4-1) + 3*4^(6-5-1)
// = 0*4^5 + 3*4^4 + 2*4^3 + 1*4^2 + 0*4^1 + 3*4^0
// = 0 + 3*256 + 2*64 + 1*16 + 0*4 + 3*1
// = 0 + 768 + 128 + 16 + 0 + 3
// = 915
int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
int kmer = 0;
for(int i=0;i<kmerSize;i++){
if(toupper(sequence[i+index]) == 'A') { kmer += (0 * power4s[kmerSize-i-1]); }
else if(toupper(sequence[i+index]) == 'C') { kmer += (1 * power4s[kmerSize-i-1]); }
else if(toupper(sequence[i+index]) == 'G') { kmer += (2 * power4s[kmerSize-i-1]); }
else if(toupper(sequence[i+index]) == 'U') { kmer += (3 * power4s[kmerSize-i-1]); }
else if(toupper(sequence[i+index]) == 'T') { kmer += (3 * power4s[kmerSize-i-1]); }
else if(toupper(sequence[i+index]) == 'N') { return (int)power4s[kmerSize]; }
}
return kmer;
}
/**************************************************************************************************/
string Kmer::getKmerBases(int kmerNumber){
// Here we convert the kmer number into the kmer in terms of bases.
//
// Example: Score = 915 (for a 6-mer)
// Base6 = (915 / 4^0) % 4 = 915 % 4 = 3 => T [T]
// Base5 = (915 / 4^1) % 4 = 228 % 4 = 0 => A [AT]
// Base4 = (915 / 4^2) % 4 = 57 % 4 = 1 => C [CAT]
// Base3 = (915 / 4^3) % 4 = 14 % 4 = 2 => G [GCAT]
// Base2 = (915 / 4^4) % 4 = 3 % 4 = 3 => T [TGCAT]
// Base1 = (915 / 4^5) % 4 = 0 % 4 = 0 => A [ATGCAT] -> this checks out with the previous method
int power4s[14] = { 1, 4, 16, 64, 256, 1024, 4096, 16384, 65536, 262144, 1048576, 4194304, 16777216, 67108864 };
string kmer = "";
if(kmerNumber == power4s[kmerSize]){//pow(4.,7)){ // if the kmer number is the same as the maxKmer then it must
for(int i=0;i<kmerSize;i++){ // have had an N in it and so we'll just call it N x kmerSize
kmer += 'N';
}
}
else{
for(int i=0;i<kmerSize;i++){
int nt = (int)(kmerNumber / (float)power4s[i]) % 4; // the '%' operator returns the remainder
if(nt == 0) { kmer = 'A' + kmer; } // from int-based division ]
else if(nt == 1){ kmer = 'C' + kmer; }
else if(nt == 2){ kmer = 'G' + kmer; }
else if(nt == 3){ kmer = 'T' + kmer; }
}
}
return kmer;
}
/**************************************************************************************************/
int Kmer::getReverseKmerNumber(int kmerNumber){
string kmerString = getKmerBases(kmerNumber);
//get Reverse
string reverse = "";
for(int i=kmerString.length()-1;i>=0;i--){
if(kmerString[i] == 'A') { reverse += 'T'; }
else if(kmerString[i] == 'T'){ reverse += 'A'; }
else if(kmerString[i] == 'G'){ reverse += 'C'; }
else if(kmerString[i] == 'C'){ reverse += 'G'; }
else { reverse += 'N'; }
}
int reverseNumber = getKmerNumber(reverse, 0);
return reverseNumber;
}
/**************************************************************************************************/
char Kmer::getASCII(int number) { return (char)(33+number); } // '!' is the first printable char and
// has the int value of 33
/**************************************************************************************************/
int Kmer::getNumber(char character) { return ((int)(character-'!')); } // '!' has the value of 33
/**************************************************************************************************/
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