int
main(int argc, char **argv)
{
int status;
ESL_RANDOMNESS *r = esl_randomness_CreateTimeseeded();
ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
ESL_SCOREMATRIX *S = NULL;
ESL_DSQ *x = NULL; /* iid query */
ESL_DSQ *y = NULL; /* iid target */
double lambda;
double bg[20]; /* iid background probabilities */
int L; /* query length */
int M; /* target length */
int nseq; /* number of target seqs to simulate */
int i;
int gop;
int gex;
char *mxfile = "PMX";
int raw_sc;
/* Configuration
*/
L = 400; /* query length */
M = 400; /* target length */
nseq = 50000;
gop = -11;
gex = -1;
lambda = 0.3207;
ESL_ALLOC(x, sizeof(ESL_DSQ) * (L+2));
ESL_ALLOC(y, sizeof(ESL_DSQ) * (M+2));
/* Input an amino acid score matrix from a file. */
if (mxfile != NULL) {
ESL_FILEPARSER *efp = NULL;
if ( esl_fileparser_Open(mxfile, &efp) != eslOK) esl_fatal("failed to open score file %s", mxfile);
if ( esl_sco_Read(efp, abc, &S) != eslOK) esl_fatal("failed to read matrix from %s", mxfile);
esl_fileparser_Close(efp);
} else { /* default = BLOSUM62 */
S = esl_scorematrix_Create(abc);
esl_scorematrix_SetBLOSUM62(S);
}
esl_composition_BL62(bg);
esl_rsq_xIID(r, bg, 20, L, x);
for (i = 0; i < nseq; i++)
{
esl_rsq_xIID(r, bg, 20, M, y);
esl_swat_Score(x, L, y, M, S, gop, gex, &raw_sc);
printf("%d\n", raw_sc);
}
free(x);
free(y);
esl_scorematrix_Destroy(S);
esl_alphabet_Destroy(abc);
esl_randomness_Destroy(r);
exit(0);
ERROR:
exit(status);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
char *qfile = esl_opt_GetArg(go, 1);
char *tfile = esl_opt_GetArg(go, 2);
ESL_SQFILE *qfp = NULL;
ESL_SQFILE *tfp = NULL;
ESL_SQ *qsq = esl_sq_CreateDigital(abc);
ESL_SQ *tsq = esl_sq_CreateDigital(abc);
ESL_SCOREMATRIX *S = esl_scorematrix_Create(abc);
ESL_DMATRIX *Q = NULL;
P7_BG *bg = p7_bg_Create(abc);
P7_HMM *hmm = NULL;
P7_PROFILE *gm = NULL;
P7_REFMX *vit = p7_refmx_Create(200, 400); /* will grow as needed */
double *fa = malloc(sizeof(double) * abc->K);
double popen = 0.02;
double pextend = 0.4;
double lambda;
float vsc;
float nullsc;
int status;
esl_composition_BL62(fa);
esl_vec_D2F(fa, abc->K, bg->f);
esl_scorematrix_Set("BLOSUM62", S);
esl_scorematrix_ProbifyGivenBG(S, fa, fa, &lambda, &Q);
esl_scorematrix_JointToConditionalOnQuery(abc, Q);
if (esl_sqfile_OpenDigital(abc, qfile, eslSQFILE_UNKNOWN, NULL, &qfp) != eslOK) esl_fatal("failed to open %s", qfile);
if (esl_sqio_Read(qfp, qsq) != eslOK) esl_fatal("failed to read query seq");
p7_Seqmodel(abc, qsq->dsq, qsq->n, qsq->name, Q, bg->f, popen, pextend, &hmm);
p7_hmm_SetComposition(hmm);
p7_hmm_SetConsensus(hmm, qsq);
gm = p7_profile_Create(hmm->M, abc);
p7_profile_ConfigUnilocal(gm, hmm, bg, 400);
if (esl_sqfile_OpenDigital(abc, tfile, eslSQFILE_UNKNOWN, NULL, &tfp) != eslOK) esl_fatal("failed to open %s", tfile);
while ((status = esl_sqio_Read(tfp, tsq)) == eslOK)
{
p7_bg_SetLength (bg, tsq->n);
p7_profile_SetLength(gm, tsq->n);
p7_ReferenceViterbi(tsq->dsq, tsq->n, gm, vit, NULL, &vsc);
p7_bg_NullOne(bg, tsq->dsq, tsq->n, &nullsc);
printf("%.4f %-25s %-25s\n", (vsc - nullsc) / eslCONST_LOG2, tsq->name, gm->name);
esl_sq_Reuse(tsq);
p7_refmx_Reuse(vit);
}
p7_refmx_Destroy(vit);
p7_profile_Destroy(gm);
p7_hmm_Destroy(hmm);
p7_bg_Destroy(bg);
esl_dmatrix_Destroy(Q);
esl_scorematrix_Destroy(S);
free(fa);
esl_sq_Destroy(qsq);
esl_sq_Destroy(tsq);
esl_sqfile_Close(qfp);
esl_sqfile_Close(tfp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
