/* Function: default_nucleic_prior()
*
* Purpose: Set the default DNA prior. (for now, almost a Laplace)
*/
static struct p7prior_s *
default_nucleic_prior(void)
{
struct p7prior_s *pri;
pri = P7AllocPrior();
pri->strategy = PRI_DCHLET;
/* The use of the Pfam-trained amino acid transition priors
* here is TOTALLY bogus. But it works better than a straight
* Laplace, esp. for Maxmodelmaker(). For example, a Laplace
* prior builds M=1 models for a single sequence GAATTC (at
* one time an open "bug").
*/
pri->tnum = 1;
pri->tq[0] = 1.;
pri->t[0][TMM] = 0.7939;
pri->t[0][TMI] = 0.0278;
pri->t[0][TMD] = 0.0135;
pri->t[0][TIM] = 0.1551;
pri->t[0][TII] = 0.1331;
pri->t[0][TDM] = 0.9002;
pri->t[0][TDD] = 0.5630;
pri->mnum = 1;
pri->mq[0] = 1.;
FSet(pri->m[0], Alphabet_size, 1.);
pri->inum = 1;
pri->iq[0] = 1.;
FSet(pri->i[0], Alphabet_size, 1.);
return pri;
}
struct p7prior_s *
default_amino_prior(void)
{
struct p7prior_s *pri;
int x, q;
static float defmq[5] = {
0.178091, 0.056591, 0.0960191, 0.0781233, 0.0834977 };
static float defm[5][6] = {
{ 0.270671, 0.039848, 0.017576, 0.016415, 0.014268, 0.216147 },
{ 0.021465, 0.010300, 0.011741, 0.010883, 0.385651, 0.029156 },
{ 0.561459, 0.045448, 0.438366, 0.764167, 0.087364, 0.583402 },
{ 0.070143, 0.011140, 0.019479, 0.094657, 0.013162, 0.073732 },
{ 0.041103, 0.014794, 0.005610, 0.010216, 0.153602, 0.012049 }
};
pri = P7AllocPrior();
pri->mnum = 5;
for (q = 0; q < pri->mnum; q++)
{
pri->mq[q] = defmq[q];
for (x = 0; x < 6; x++)
pri->m[q][x] = defm[q][x];
}
return pri;
}
/* Function: P7LaplacePrior()
*
* Purpose: Create a Laplace plus-one prior. (single component Dirichlets).
* Global alphabet info is assumed to have been set already.
*
* Args: (void)
*
* Return: prior. Allocated here; call FreePrior() to free it.
*/
struct p7prior_s *
P7LaplacePrior(void)
{
struct p7prior_s *pri;
pri = P7AllocPrior();
pri->strategy = PRI_DCHLET;
pri->tnum = 1;
pri->tq[0] = 1.;
FSet(pri->t[0], 8, 1.);
pri->mnum = 1;
pri->mq[0] = 1.;
FSet(pri->m[0], Alphabet_size, 1.);
pri->inum = 1;
pri->iq[0] = 1.;
FSet(pri->i[0], Alphabet_size, 1.);
return pri;
}
/* Function: P7ReadPrior()
*
* Purpose: Input a prior from disk file.
*/
struct p7prior_s *
P7ReadPrior(char *prifile)
{
FILE *fp;
struct p7prior_s *pri;
char *sptr;
int q, x;
if ((fp = fopen(prifile, "r")) == NULL)
Die("Failed to open HMMER prior file %s\n", prifile);
pri = P7AllocPrior();
/* First entry is the strategy:
* Only standard Dirichlet prior (simple or mixture) is supported in Plan7 so far
*/
sptr = Getword(fp, sqdARG_STRING);
s2upper(sptr);
if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET;
else Die("No such prior strategy %s; failed to parse file %s", sptr, prifile);
/* Second entry is the alphabet type:
* Amino or Nucleic
*/
sptr = Getword(fp, sqdARG_STRING);
s2upper(sptr);
if (strcmp(sptr, "AMINO") == 0)
{
if (Alphabet_type != hmmAMINO)
Die("HMM and/or sequences are DNA/RNA; can't use protein prior %s", prifile);
}
else if (strcmp(sptr, "NUCLEIC") == 0)
{
if (Alphabet_type != hmmNUCLEIC)
Die("HMM and/or sequences are protein; can't use DNA/RNA prior %s", prifile);
}
else
Die("Alphabet \"%s\" in prior file %s isn't valid.", sptr, prifile);
/* State transition priors:
* # of mixtures.
* then for each mixture:
* prior P(q)
* Dirichlet terms for Tmm, Tmi, Tmd, Tim, Tii, Tid, Tdm, Tdi, Tdd
*/
pri->tnum = atoi(Getword(fp, sqdARG_INT));
if (pri->tnum < 0)
Die("%d is bad; need at least one state transition mixture component", pri->tnum);
if (pri->tnum > MAXDCHLET)
Die("%d is bad, too many transition components (MAXDCHLET = %d)\n", MAXDCHLET);
for (q = 0; q < pri->tnum; q++)
{
pri->tq[q] = (float) atof(Getword(fp, sqdARG_FLOAT));
for (x = 0; x < 7; x++)
pri->t[q][x] = (float) atof(Getword(fp, sqdARG_FLOAT));
}
/* Match emission priors:
* # of mixtures.
* then for each mixture:
* prior P(q)
* Dirichlet terms for Alphabet_size symbols in Alphabet
*/
pri->mnum = atoi(Getword(fp, sqdARG_INT));
if (pri->mnum < 0)
Die("%d is bad; need at least one match emission mixture component", pri->mnum);
if (pri->mnum > MAXDCHLET)
Die("%d is bad; too many match components (MAXDCHLET = %d)\n", pri->mnum, MAXDCHLET);
for (q = 0; q < pri->mnum; q++)
{
pri->mq[q] = (float) atof(Getword(fp, sqdARG_FLOAT));
for (x = 0; x < Alphabet_size; x++)
pri->m[q][x] = (float) atof(Getword(fp, sqdARG_FLOAT));
}
/* Insert emission priors:
* # of mixtures.
* then for each mixture component:
* prior P(q)
* Dirichlet terms for Alphabet_size symbols in Alphabet
*/
pri->inum = atoi(Getword(fp, sqdARG_INT));
if (pri->inum < 0)
Die("%d is bad; need at least one insert emission mixture component", pri->inum);
if (pri->inum > MAXDCHLET)
Die("%d is bad; too many insert components (MAXDCHLET = %d)\n", pri->inum, MAXDCHLET);
for (q = 0; q < pri->inum; q++)
{
pri->iq[q] = (float) atof(Getword(fp, sqdARG_FLOAT));
for (x = 0; x < Alphabet_size; x++)
pri->i[q][x] = (float) atof(Getword(fp, sqdARG_FLOAT));
}
fclose(fp);
return pri;
}
/* Function: default_amino_prior()
*
* Purpose: Set the default protein prior.
*/
static struct p7prior_s *
default_amino_prior(void)
{
struct p7prior_s *pri;
int q, x;
/* default match mixture coefficients */
static float defmq[9] = {
0.178091, 0.056591, 0.0960191, 0.0781233, 0.0834977,
0.0904123, 0.114468, 0.0682132, 0.234585 };
/* default match mixture Dirichlet components */
static float defm[9][20] = {
{ 0.270671, 0.039848, 0.017576, 0.016415, 0.014268,
0.131916, 0.012391, 0.022599, 0.020358, 0.030727,
0.015315, 0.048298, 0.053803, 0.020662, 0.023612,
0.216147, 0.147226, 0.065438, 0.003758, 0.009621 },
{ 0.021465, 0.010300, 0.011741, 0.010883, 0.385651,
0.016416, 0.076196, 0.035329, 0.013921, 0.093517,
0.022034, 0.028593, 0.013086, 0.023011, 0.018866,
0.029156, 0.018153, 0.036100, 0.071770, 0.419641 },
{ 0.561459, 0.045448, 0.438366, 0.764167, 0.087364,
0.259114, 0.214940, 0.145928, 0.762204, 0.247320,
0.118662, 0.441564, 0.174822, 0.530840, 0.465529,
0.583402, 0.445586, 0.227050, 0.029510, 0.121090 },
{ 0.070143, 0.011140, 0.019479, 0.094657, 0.013162,
0.048038, 0.077000, 0.032939, 0.576639, 0.072293,
0.028240, 0.080372, 0.037661, 0.185037, 0.506783,
0.073732, 0.071587, 0.042532, 0.011254, 0.028723 },
{ 0.041103, 0.014794, 0.005610, 0.010216, 0.153602,
0.007797, 0.007175, 0.299635, 0.010849, 0.999446,
0.210189, 0.006127, 0.013021, 0.019798, 0.014509,
0.012049, 0.035799, 0.180085, 0.012744, 0.026466 },
{ 0.115607, 0.037381, 0.012414, 0.018179, 0.051778,
0.017255, 0.004911, 0.796882, 0.017074, 0.285858,
0.075811, 0.014548, 0.015092, 0.011382, 0.012696,
0.027535, 0.088333, 0.944340, 0.004373, 0.016741 },
{ 0.093461, 0.004737, 0.387252, 0.347841, 0.010822,
0.105877, 0.049776, 0.014963, 0.094276, 0.027761,
0.010040, 0.187869, 0.050018, 0.110039, 0.038668,
0.119471, 0.065802, 0.025430, 0.003215, 0.018742 },
{ 0.452171, 0.114613, 0.062460, 0.115702, 0.284246,
0.140204, 0.100358, 0.550230, 0.143995, 0.700649,
0.276580, 0.118569, 0.097470, 0.126673, 0.143634,
0.278983, 0.358482, 0.661750, 0.061533, 0.199373 },
{ 0.005193, 0.004039, 0.006722, 0.006121, 0.003468,
0.016931, 0.003647, 0.002184, 0.005019, 0.005990,
0.001473, 0.004158, 0.009055, 0.003630, 0.006583,
0.003172, 0.003690, 0.002967, 0.002772, 0.002686 },
};
pri = P7AllocPrior();
pri->strategy = PRI_DCHLET;
/* Transition priors are subjective, but borrowed from GJM's estimations
* on Pfam
*/
pri->tnum = 1;
pri->tq[0] = 1.0;
pri->t[0][TMM] = 0.7939;
pri->t[0][TMI] = 0.0278; /* Markus suggests: ~10x MD: ~0.036: test! */
pri->t[0][TMD] = 0.0135; /* Markus suggests: ~0.1x MI: ~0.004 */
pri->t[0][TIM] = 0.1551;
pri->t[0][TII] = 0.1331;
pri->t[0][TDM] = 0.9002;
pri->t[0][TDD] = 0.5630;
/* Match emission priors are a mixture Dirichlet,
* from Kimmen Sjolander (Blocks9)
*/
pri->mnum = 9;
for (q = 0; q < pri->mnum; q++)
{
pri->mq[q] = defmq[q];
for (x = 0; x < 20; x++)
pri->m[q][x] = defm[q][x];
}
/* These insert emission priors are subjective. Observed frequencies
* were obtained from PFAM 1.0, 10 Nov 96;
* see ~/projects/plan7/InsertStatistics.
* Inserts are slightly biased towards polar residues and away from
* hydrophobic residues.
*/
pri->inum = 1;
pri->iq[0] = 1.;
pri->i[0][0] = 681.; /* A */
pri->i[0][1] = 120.; /* C */
pri->i[0][2] = 623.; /* D */
pri->i[0][3] = 651.; /* E */
pri->i[0][4] = 313.; /* F */
pri->i[0][5] = 902.; /* G */
pri->i[0][6] = 241.; /* H */
pri->i[0][7] = 371.; /* I */
pri->i[0][8] = 687.; /* K */
pri->i[0][9] = 676.; /* L */
pri->i[0][10] = 143.; /* M */
pri->i[0][11] = 548.; /* N */
pri->i[0][12] = 647.; /* P */
pri->i[0][13] = 415.; /* Q */
pri->i[0][14] = 551.; /* R */
pri->i[0][15] = 926.; /* S */
pri->i[0][16] = 623.; /* T */
pri->i[0][17] = 505.; /* V */
pri->i[0][18] = 102.; /* W */
pri->i[0][19] = 269.; /* Y */
return pri;
}