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#include "muscle.h"
#include "distfunc.h"
#include "seqvect.h"
#include <math.h>
#define TRACE 0
#define MIN(x, y) (((x) < (y)) ? (x) : (y))
#define MAX(x, y) (((x) > (y)) ? (x) : (y))
const unsigned TUPLE_COUNT = 6*6*6*6*6*6;
static unsigned char Count1[TUPLE_COUNT];
static unsigned char Count2[TUPLE_COUNT];
// Amino acid groups according to MAFFT (sextet5)
// 0 = A G P S T
// 1 = I L M V
// 2 = N D Q E B Z
// 3 = R H K
// 4 = F W Y
// 5 = C
// 6 = X . - U
unsigned ResidueGroup[] =
{
0, // AX_A,
5, // AX_C,
2, // AX_D,
2, // AX_E,
4, // AX_F,
0, // AX_G,
3, // AX_H,
1, // AX_I,
3, // AX_K,
1, // AX_L,
1, // AX_M,
2, // AX_N,
0, // AX_P,
2, // AX_Q,
3, // AX_R,
0, // AX_S,
0, // AX_T,
1, // AX_V,
4, // AX_W,
4, // AX_Y,
2, // AX_B, // D or N
2, // AX_Z, // E or Q
0, // AX_X, // Unknown // ******** TODO *************
// This isn't the correct way of avoiding group 6
0 // AX_GAP, // ******** TODO ******************
};
unsigned uResidueGroupCount = sizeof(ResidueGroup)/sizeof(ResidueGroup[0]);
static char *TupleToStr(int t)
{
static char s[7];
int t1, t2, t3, t4, t5, t6;
t1 = t%6;
t2 = (t/6)%6;
t3 = (t/(6*6))%6;
t4 = (t/(6*6*6))%6;
t5 = (t/(6*6*6*6))%6;
t6 = (t/(6*6*6*6*6))%6;
s[5] = '0' + t1;
s[4] = '0' + t2;
s[3] = '0' + t3;
s[2] = '0' + t4;
s[1] = '0' + t5;
s[0] = '0' + t6;
return s;
}
static unsigned GetTuple(const unsigned uLetters[], unsigned n)
{
assert(uLetters[n] < uResidueGroupCount);
assert(uLetters[n+1] < uResidueGroupCount);
assert(uLetters[n+2] < uResidueGroupCount);
assert(uLetters[n+3] < uResidueGroupCount);
assert(uLetters[n+4] < uResidueGroupCount);
assert(uLetters[n+5] < uResidueGroupCount);
unsigned u1 = ResidueGroup[uLetters[n]];
unsigned u2 = ResidueGroup[uLetters[n+1]];
unsigned u3 = ResidueGroup[uLetters[n+2]];
unsigned u4 = ResidueGroup[uLetters[n+3]];
unsigned u5 = ResidueGroup[uLetters[n+4]];
unsigned u6 = ResidueGroup[uLetters[n+5]];
return u6 + u5*6 + u4*6*6 + u3*6*6*6 + u2*6*6*6*6 + u1*6*6*6*6*6;
}
static void CountTuples(const unsigned L[], unsigned uTupleCount, unsigned char Count[])
{
memset(Count, 0, TUPLE_COUNT*sizeof(unsigned char));
for (unsigned n = 0; n < uTupleCount; ++n)
{
const unsigned uTuple = GetTuple(L, n);
++(Count[uTuple]);
}
}
static void ListCount(const unsigned char Count[])
{
for (unsigned n = 0; n < TUPLE_COUNT; ++n)
{
if (0 == Count[n])
continue;
Log("%s %u\n", TupleToStr(n), Count[n]);
}
}
void DistKmer6_6(const SeqVect &v, DistFunc &DF)
{
const unsigned uSeqCount = v.Length();
DF.SetCount(uSeqCount);
if (0 == uSeqCount)
return;
// Initialize distance matrix to zero
for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1)
{
DF.SetDist(uSeq1, uSeq1, 0);
for (unsigned uSeq2 = 0; uSeq2 < uSeq1; ++uSeq2)
DF.SetDist(uSeq1, uSeq2, 0);
}
// Convert to letters
unsigned **Letters = new unsigned *[uSeqCount];
for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
{
Seq &s = *(v[uSeqIndex]);
const unsigned uSeqLength = s.Length();
unsigned *L = new unsigned[uSeqLength];
Letters[uSeqIndex] = L;
for (unsigned n = 0; n < uSeqLength; ++n)
{
char c = s[n];
L[n] = CharToLetterEx(c);
assert(L[n] < uResidueGroupCount);
}
}
unsigned **uCommonTupleCount = new unsigned *[uSeqCount];
for (unsigned n = 0; n < uSeqCount; ++n)
{
uCommonTupleCount[n] = new unsigned[uSeqCount];
memset(uCommonTupleCount[n], 0, uSeqCount*sizeof(unsigned));
}
const unsigned uPairCount = (uSeqCount*(uSeqCount + 1))/2;
unsigned uCount = 0;
for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1)
{
Seq &seq1 = *(v[uSeq1]);
const unsigned uSeqLength1 = seq1.Length();
if (uSeqLength1 < 5)
continue;
const unsigned uTupleCount = uSeqLength1 - 5;
const unsigned *L = Letters[uSeq1];
CountTuples(L, uTupleCount, Count1);
#if TRACE
{
Log("Seq1=%d\n", uSeq1);
Log("Groups:\n");
for (unsigned n = 0; n < uSeqLength1; ++n)
Log("%u", ResidueGroup[L[n]]);
Log("\n");
Log("Tuples:\n");
ListCount(Count1);
}
#endif
SetProgressDesc("K-mer dist pass 1");
for (unsigned uSeq2 = 0; uSeq2 <= uSeq1; ++uSeq2)
{
if (0 == uCount%500)
Progress(uCount, uPairCount);
++uCount;
Seq &seq2 = *(v[uSeq2]);
const unsigned uSeqLength2 = seq2.Length();
if (uSeqLength2 < 5)
{
if (uSeq1 == uSeq2)
DF.SetDist(uSeq1, uSeq2, 0);
else
DF.SetDist(uSeq1, uSeq2, 1);
continue;
}
// First pass through seq 2 to count tuples
const unsigned uTupleCount = uSeqLength2 - 5;
const unsigned *L = Letters[uSeq2];
CountTuples(L, uTupleCount, Count2);
#if TRACE
Log("Seq2=%d Counts=\n", uSeq2);
ListCount(Count2);
#endif
// Second pass to accumulate sum of shared tuples
// MAFFT defines this as the sum over unique tuples
// in seq2 of the minimum of the number of tuples found
// in the two sequences.
unsigned uSum = 0;
for (unsigned n = 0; n < uTupleCount; ++n)
{
const unsigned uTuple = GetTuple(L, n);
uSum += MIN(Count1[uTuple], Count2[uTuple]);
// This is a hack to make sure each unique tuple counted only once.
Count2[uTuple] = 0;
}
#if TRACE
{
Seq &s1 = *(v[uSeq1]);
Seq &s2 = *(v[uSeq2]);
const char *pName1 = s1.GetName();
const char *pName2 = s2.GetName();
Log("Common count %s(%d) - %s(%d) =%u\n",
pName1, uSeq1, pName2, uSeq2, uSum);
}
#endif
uCommonTupleCount[uSeq1][uSeq2] = uSum;
uCommonTupleCount[uSeq2][uSeq1] = uSum;
}
}
ProgressStepsDone();
uCount = 0;
SetProgressDesc("K-mer dist pass 2");
for (unsigned uSeq1 = 0; uSeq1 < uSeqCount; ++uSeq1)
{
Seq &s1 = *(v[uSeq1]);
const char *pName1 = s1.GetName();
double dCommonTupleCount11 = uCommonTupleCount[uSeq1][uSeq1];
if (0 == dCommonTupleCount11)
dCommonTupleCount11 = 1;
DF.SetDist(uSeq1, uSeq1, 0);
for (unsigned uSeq2 = 0; uSeq2 < uSeq1; ++uSeq2)
{
if (0 == uCount%500)
Progress(uCount, uPairCount);
++uCount;
double dCommonTupleCount22 = uCommonTupleCount[uSeq2][uSeq2];
if (0 == dCommonTupleCount22)
dCommonTupleCount22 = 1;
const double dDist1 = 3.0*(dCommonTupleCount11 - uCommonTupleCount[uSeq1][uSeq2])
/dCommonTupleCount11;
const double dDist2 = 3.0*(dCommonTupleCount22 - uCommonTupleCount[uSeq1][uSeq2])
/dCommonTupleCount22;
// dMinDist is the value used for tree-building in MAFFT
const double dMinDist = MIN(dDist1, dDist2);
DF.SetDist(uSeq1, uSeq2, (float) dMinDist);
//const double dEstimatedPctId = TupleDistToEstimatedPctId(dMinDist);
//g_dfPwId.SetDist(uSeq1, uSeq2, dEstimatedPctId);
// **** TODO **** why does this make score slightly worse??
//const double dKimuraDist = KimuraDist(dEstimatedPctId);
//DF.SetDist(uSeq1, uSeq2, dKimuraDist);
}
}
ProgressStepsDone();
for (unsigned n = 0; n < uSeqCount; ++n)
delete[] uCommonTupleCount[n];
delete[] uCommonTupleCount;
delete[] Letters;
}
double PctIdToMAFFTDist(double dPctId)
{
if (dPctId < 0.05)
dPctId = 0.05;
double dDist = -log(dPctId);
return dDist;
}
double PctIdToHeightMAFFT(double dPctId)
{
return PctIdToMAFFTDist(dPctId);
}
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