/* utest_basic()
* An MSA to ex{e,o}rcise past demons.
* 1. seq2 gives an I->end transition.
* 2. seq1 contains degenerate Z,X, exercising symbol counting
* of degenerate residues.
*/
static void
utest_basic(void)
{
char *failmsg = "failure in build.c::utest_basic() unit test";
char msafile[16] = "p7tmpXXXXXX"; /* tmpfile name template */
FILE *ofp = NULL;
ESL_ALPHABET *abc = esl_alphabet_Create(eslAMINO);
ESL_MSAFILE *afp = NULL;
ESL_MSA *msa = NULL;
P7_HMM *hmm = NULL;
float symfrac = 0.5;
if (esl_tmpfile_named(msafile, &ofp) != eslOK) esl_fatal(failmsg);
fprintf(ofp, "# STOCKHOLM 1.0\n");
fprintf(ofp, "#=GC RF --xxxxxxxxxxxxxxxx-xxx-x--\n");
fprintf(ofp, "seq1 --ACDEFGHIKLMNPZXS-TVW-Yyy\n");
fprintf(ofp, "seq2 aaACDEFGHIKLMNPQRS-TVWw---\n");
fprintf(ofp, "seq3 aaAC-EFGHIKLMNPQRS-TVW-Y--\n");
fprintf(ofp, "seq4 aaAC-EFGHIKLMNPQRS-TVW-Y--\n");
fprintf(ofp, "//\n");
fclose(ofp);
if (esl_msafile_Open(&abc, msafile, NULL, eslMSAFILE_UNKNOWN, NULL, &afp) != eslOK) esl_fatal(failmsg);
if (esl_msafile_Read(afp, &msa) != eslOK) esl_fatal(failmsg);
if (p7_Fastmodelmaker(msa, symfrac, NULL, &hmm, NULL) != eslOK) esl_fatal(failmsg);
p7_hmm_Destroy(hmm);
esl_msa_Destroy(msa);
esl_msafile_Close(afp);
esl_alphabet_Destroy(abc);
remove(msafile);
return;
}
/* build_model():
* Given <msa>, choose HMM architecture, collect counts;
* upon return, <*ret_hmm> is newly allocated and contains
* relative-weighted observed counts.
* Optionally, caller can request an array of inferred traces for
* the <msa> too.
*/
static int
build_model(P7_BUILDER *bld, ESL_MSA *msa, P7_HMM **ret_hmm, P7_TRACE ***opt_tr)
{
int status;
if (bld->arch_strategy == p7_ARCH_FAST)
{
status = p7_Fastmodelmaker( msa, bld->symfrac, bld, ret_hmm, opt_tr);
if (status == eslENORESULT) ESL_XFAIL(status, bld->errbuf, "Alignment %s has no consensus columns w/ > %d%% residues - can't build a model.\n", msa->name != NULL ? msa->name : "", (int) (100 * bld->symfrac));
else if (status == eslEMEM) ESL_XFAIL(status, bld->errbuf, "Memory allocation failure in model construction.\n");
else if (status != eslOK) ESL_XFAIL(status, bld->errbuf, "internal error in model construction.\n");
}
else if (bld->arch_strategy == p7_ARCH_HAND)
{
status = p7_Handmodelmaker( msa, bld, ret_hmm, opt_tr);
if (status == eslENORESULT) ESL_XFAIL(status, bld->errbuf, "Alignment %s has no annotated consensus columns - can't build a model.\n", msa->name != NULL ? msa->name : "");
else if (status == eslEFORMAT) ESL_XFAIL(status, bld->errbuf, "Alignment %s has no reference annotation line\n", msa->name != NULL ? msa->name : "");
else if (status == eslEMEM) ESL_XFAIL(status, bld->errbuf, "Memory allocation failure in model construction.\n");
else if (status != eslOK) ESL_XFAIL(status, bld->errbuf, "internal error in model construction.\n");
}
return eslOK;
ERROR:
return status;
}
/* The "basic" utest is a minimal driver for making a small DNA profile and a small DNA sequence,
* then running Viterbi and Forward. It's useful for dumping DP matrices and profiles for debugging.
*/
static void
utest_basic(ESL_GETOPTS *go)
{
char *query= "# STOCKHOLM 1.0\n\nseq1 GAATTC\nseq2 GAATTC\n//\n";
int fmt = eslMSAFILE_STOCKHOLM;
char *targ = "GAATTC";
ESL_ALPHABET *abc = NULL;
ESL_MSA *msa = NULL;
P7_HMM *hmm = NULL;
P7_PROFILE *gm = NULL;
P7_BG *bg = NULL;
P7_PRIOR *pri = NULL;
ESL_DSQ *dsq = NULL;
P7_GMX *gx = NULL;
P7_TRACE *tr = NULL;
int L = strlen(targ);
float vsc, vsc2, fsc;
if ((abc = esl_alphabet_Create(eslDNA)) == NULL) esl_fatal("failed to create alphabet");
if ((pri = p7_prior_CreateNucleic()) == NULL) esl_fatal("failed to create prior");
if ((msa = esl_msa_CreateFromString(query, fmt)) == NULL) esl_fatal("failed to create MSA");
if (esl_msa_Digitize(abc, msa, NULL) != eslOK) esl_fatal("failed to digitize MSA");
if (p7_Fastmodelmaker(msa, 0.5, NULL, &hmm, NULL) != eslOK) esl_fatal("failed to create GAATTC model");
if (p7_ParameterEstimation(hmm, pri) != eslOK) esl_fatal("failed to parameterize GAATTC model");
if (p7_hmm_SetConsensus(hmm, NULL) != eslOK) esl_fatal("failed to make consensus");
if ((bg = p7_bg_Create(abc)) == NULL) esl_fatal("failed to create DNA null model");
if ((gm = p7_profile_Create(hmm->M, abc)) == NULL) esl_fatal("failed to create GAATTC profile");
if (p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL)!= eslOK) esl_fatal("failed to config profile");
if (p7_profile_Validate(gm, NULL, 0.0001) != eslOK) esl_fatal("whoops, profile is bad!");
if (esl_abc_CreateDsq(abc, targ, &dsq) != eslOK) esl_fatal("failed to create GAATTC digital sequence");
if ((gx = p7_gmx_Create(gm->M, L)) == NULL) esl_fatal("failed to create DP matrix");
if ((tr = p7_trace_Create()) == NULL) esl_fatal("trace creation failed");
p7_GViterbi (dsq, L, gm, gx, &vsc);
if (esl_opt_GetBoolean(go, "-v")) printf("Viterbi score: %.4f\n", vsc);
if (esl_opt_GetBoolean(go, "-v")) p7_gmx_Dump(stdout, gx, p7_DEFAULT);
p7_GTrace (dsq, L, gm, gx, tr);
p7_trace_Score(tr, dsq, gm, &vsc2);
if (esl_opt_GetBoolean(go, "-v")) p7_trace_Dump(stdout, tr, gm, dsq);
if (esl_FCompare(vsc, vsc2, 1e-5) != eslOK) esl_fatal("trace score and Viterbi score don't agree.");
p7_GForward (dsq, L, gm, gx, &fsc);
if (esl_opt_GetBoolean(go, "-v")) printf("Forward score: %.4f\n", fsc);
if (esl_opt_GetBoolean(go, "-v")) p7_gmx_Dump(stdout, gx, p7_DEFAULT);
p7_trace_Destroy(tr);
p7_gmx_Destroy(gx);
free(dsq);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_msa_Destroy(msa);
p7_prior_Destroy(pri);
esl_alphabet_Destroy(abc);
return;
}
