int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *alifile = NULL; /* alignment file name */
int infmt = eslMSAFILE_UNKNOWN; /* format code for alifile */
int outfmt = eslMSAFILE_UNKNOWN; /* output format for fetched msa's */
ESLX_MSAFILE *afp = NULL; /* open alignment file */
FILE *ofp = NULL; /* output stream for alignments */
int status; /* easel return code */
/***********************************************
* Parse command line
***********************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) < 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
if (esl_opt_IsOn(go, "--informat")) {
infmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslMSAFILE_UNKNOWN) esl_fatal("%s is not a valid input alignment file format for --informat", esl_opt_GetString(go, "--informat"));
}
outfmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--outformat"));
if (outfmt == eslMSAFILE_UNKNOWN) esl_fatal("%s is not a valid output alignment file format for --outformat", esl_opt_GetString(go, "--outformat"));
alifile = esl_opt_GetArg(go, 1);
/* Open the alignment file. */
if ( (status = eslx_msafile_Open(NULL, alifile, NULL, infmt, NULL, &afp)) != eslOK)
eslx_msafile_OpenFailure(afp, status);
/* Open the SSI index, if any */
if (! esl_opt_GetBoolean(go, "--index"))
{
if (afp->bf->mode_is == eslBUFFER_FILE ||
afp->bf->mode_is == eslBUFFER_ALLFILE ||
afp->bf->mode_is == eslBUFFER_MMAP)
{
char *ssifile = NULL;
esl_sprintf(&ssifile, "%s.ssi", afp->bf->filename);
status = esl_ssi_Open(ssifile, &(afp->ssi));
if (status == eslERANGE ) esl_fatal("SSI index %s has 64-bit offsets; this system doesn't support them", ssifile);
else if (status == eslEFORMAT) esl_fatal("SSI index %s has an unrecognized format. Try recreating, w/ esl-afetch --index", ssifile);
else if (status == eslENOTFOUND) afp->ssi = NULL;
else if (status != eslOK) esl_fatal("SSI index %s: open failed, error code %d\n", ssifile, status);
free(ssifile);
}
}
/* Open the output file, if any
*/
if (esl_opt_GetBoolean(go, "-O"))
{
if ((ofp = fopen(esl_opt_GetArg(go, 2), "w")) == NULL)
esl_fatal("Failed to open output file %s\n", esl_opt_GetArg(go, 2));
}
else if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
esl_fatal("Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/* Hand off control flow as appropriate */
if (esl_opt_GetBoolean(go, "--index"))
{
if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
create_ssi_index(go, afp);
}
else if (esl_opt_GetBoolean(go, "-f"))
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
multifetch(go, ofp, outfmt, esl_opt_GetArg(go, 2), afp);
}
else
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
onefetch(go, ofp, outfmt, esl_opt_GetArg(go, 2), afp);
if (ofp != stdout) printf("\n\nRetrieved alignment %s.\n", esl_opt_GetArg(go, 2));
}
eslx_msafile_Close(afp);
esl_getopts_Destroy(go);
exit(0);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_GMX *gx1 = NULL;
P7_GMX *gx2 = NULL;
P7_OMX *ox1 = NULL;
P7_OMX *ox2 = NULL;
P7_TRACE *tr = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float fsc, bsc, accscore;
float fsc_g, bsc_g, accscore_g;
double Mcs;
p7_FLogsumInit();
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc); p7_bg_SetLength(bg, L);
gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om);
p7_oprofile_ReconfigLength(om, L);
if (esl_opt_GetBoolean(go, "-x") && p7_FLogsumError(-0.4, -0.5) > 0.0001)
p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode");
ox1 = p7_omx_Create(gm->M, L, L);
ox2 = p7_omx_Create(gm->M, L, L);
tr = p7_trace_CreateWithPP();
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_Forward (dsq, L, om, ox1, &fsc);
p7_Backward(dsq, L, om, ox1, ox2, &bsc);
p7_Decoding(om, ox1, ox2, ox2);
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
p7_OptimalAccuracy(om, ox2, ox1, &accscore);
if (! esl_opt_GetBoolean(go, "--notrace"))
{
p7_OATrace(om, ox2, ox1, tr);
p7_trace_Reuse(tr);
}
}
esl_stopwatch_Stop(w);
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x") )
{
gx1 = p7_gmx_Create(gm->M, L);
gx2 = p7_gmx_Create(gm->M, L);
p7_GForward (dsq, L, gm, gx1, &fsc_g);
p7_GBackward(dsq, L, gm, gx2, &bsc_g);
p7_GDecoding(gm, gx1, gx2, gx2);
p7_GOptimalAccuracy(gm, gx2, gx1, &accscore_g);
printf("generic: fwd=%8.4f bck=%8.4f acc=%8.4f\n", fsc_g, bsc_g, accscore_g);
printf("VMX: fwd=%8.4f bck=%8.4f acc=%8.4f\n", fsc, bsc, accscore);
p7_gmx_Destroy(gx1);
p7_gmx_Destroy(gx2);
}
free(dsq);
p7_omx_Destroy(ox1);
p7_omx_Destroy(ox2);
p7_trace_Destroy(tr);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_OMX *ox1 = NULL;
P7_OMX *ox2 = NULL;
P7_GMX *gx = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
P7_TRACE *tr = NULL;
int format = eslSQFILE_UNKNOWN;
char errbuf[eslERRBUFSIZE];
float fsc, bsc;
float accscore;
int status;
/* Read in one HMM */
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
p7_hmmfile_Close(hfp);
/* Read in one sequence */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
if (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");
esl_sqfile_Close(sqfp);
/* Configure a profile from the HMM */
bg = p7_bg_Create(abc); p7_bg_SetLength(bg, sq->n);
gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL); /* multihit local: H3 default */
om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om);
/* Allocations */
ox1 = p7_omx_Create(gm->M, sq->n, sq->n);
ox2 = p7_omx_Create(gm->M, sq->n, sq->n);
gx = p7_gmx_Create(gm->M, sq->n);
tr = p7_trace_CreateWithPP();
p7_FLogsumInit();
/* Run Forward, Backward; do OA fill and trace */
p7_Forward (sq->dsq, sq->n, om, ox1, &fsc);
p7_Backward(sq->dsq, sq->n, om, ox1, ox2, &bsc);
p7_Decoding(om, ox1, ox2, ox2); /* <gx2> is now the posterior decoding matrix */
p7_OptimalAccuracy(om, ox2, ox1, &accscore); /* <gx1> is now the OA matrix */
p7_OATrace(om, ox2, ox1, tr);
if (esl_opt_GetBoolean(go, "-d")) { p7_omx_FDeconvert(ox2, gx); p7_gmx_Dump(stdout, gx); }
if (esl_opt_GetBoolean(go, "-m")) { p7_omx_FDeconvert(ox1, gx); p7_gmx_Dump(stdout, gx); }
p7_trace_Dump(stdout, tr, gm, sq->dsq);
if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) p7_Die("trace fails validation:\n%s\n", errbuf);
printf("fwd = %.4f nats\n", fsc);
printf("bck = %.4f nats\n", bsc);
printf("acc = %.4f (%.2f%%)\n", accscore, accscore * 100. / (float) sq->n);
/* Cleanup */
esl_sq_Destroy(sq);
p7_trace_Destroy(tr);
p7_omx_Destroy(ox1);
p7_omx_Destroy(ox2);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
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 *hmmfile = esl_opt_GetArg(go, 1);
char *qfile = esl_opt_GetArg(go, 2);
ESL_SQ *qsq = esl_sq_CreateDigital(abc);
ESL_SQFILE *qfp = NULL;
FILE *hmmfp = NULL;
ESL_SCOREMATRIX *S = esl_scorematrix_Create(abc);
ESL_DMATRIX *Q = NULL;
P7_BG *bg = p7_bg_Create(abc);
P7_HMM *hmm = NULL;
double *fa = NULL;
double popen = esl_opt_GetReal (go, "-q");
double pextend = esl_opt_GetReal (go, "-r");
char *mxfile = esl_opt_GetString(go, "-m");
char errbuf[eslERRBUFSIZE];
double slambda;
int a,b;
int status;
/* Reverse engineer a scoring matrix to obtain conditional prob's
* that we'll use for the single-seq query HMM. Because score mx is
* symmetric, we can set up P[a][b] = P(b | a), so we can use the
* matrix rows as HMM match emission vectors. This means dividing
* the joint probs through by f_a.
*/
if (mxfile == NULL) {
if (esl_scorematrix_Set("BLOSUM62", S) != eslOK) esl_fatal("failed to set BLOSUM62 scores");
} else {
ESL_FILEPARSER *efp = NULL;
if ( esl_fileparser_Open(mxfile, NULL, &efp) != eslOK) esl_fatal("failed to open score file %s", mxfile);
if ( esl_scorematrix_Read(efp, abc, &S) != eslOK) esl_fatal("failed to read matrix from %s", mxfile);
esl_fileparser_Close(efp);
}
/* A wasteful conversion of the HMMER single-precision background probs to Easel double-prec */
ESL_ALLOC(fa, sizeof(double) * bg->abc->K);
esl_vec_F2D(bg->f, bg->abc->K, fa);
/* Backcalculate joint probabilities Q, given score matrix S and background frequencies fa */
status = esl_scorematrix_ProbifyGivenBG(S, fa, fa, &slambda, &Q);
if (status == eslEINVAL) esl_fatal("built-in score matrix %s has no valid solution for lambda", matrix);
else if (status == eslENOHALT) esl_fatal("failed to solve score matrix %s for lambda", matrix);
else if (status != eslOK) esl_fatal("unexpected error in solving score matrix %s for probability parameters", matrix);
esl_scorematrix_JointToConditionalOnQuery(abc, Q);
/* Open the query sequence file in FASTA format */
status = esl_sqfile_Open(qfile, eslSQFILE_FASTA, NULL, &qfp);
if (status == eslENOTFOUND) esl_fatal("No such file %s.", qfile);
else if (status == eslEFORMAT) esl_fatal("Format of %s unrecognized.", qfile);
else if (status == eslEINVAL) esl_fatal("Can't autodetect stdin or .gz.");
else if (status != eslOK) esl_fatal("Open of %s failed, code %d.", qfile, status);
/* Open the output HMM file */
if ((hmmfp = fopen(hmmfile, "w")) == NULL) esl_fatal("Failed to open output HMM file %s", hmmfile);
/* For each sequence, build a model and save it.
*/
while ((status = esl_sqio_Read(qfp, qsq)) == eslOK)
{
p7_Seqmodel(abc, qsq->dsq, qsq->n, qsq->name, Q, bg->f, popen, pextend, &hmm);
if ( p7_hmm_Validate(hmm, errbuf, 1e-5) != eslOK) esl_fatal("HMM validation failed: %s\n", errbuf);
if ( p7_hmmfile_WriteASCII(hmmfp, -1, hmm) != eslOK) esl_fatal("HMM save failed");
p7_hmm_Destroy(hmm);
}
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s line %" PRId64 "):\n%s\n",
qfp->filename, qfp->linenumber, qfp->errbuf);
else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
status, qfp->filename);
esl_dmatrix_Destroy(Q);
esl_scorematrix_Destroy(S);
free(fa);
free(fb);
esl_sq_Destroy(qsq);
esl_sqfile_Close(qfp);
fclose(hmmfp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_STOPWATCH *w;
ESL_GETOPTS *go;
char *msafile;
ESL_MSAFILE *afp;
ESL_MSA *msa;
int do_gsc;
int do_pb;
int do_blosum;
int maxN;
double maxid;
double cpu;
/* Process command line
*/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) esl_fatal("failed to parse cmd line: %s", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) esl_fatal("failed to parse cmd line: %s", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") == TRUE) {
puts(usage);
puts("\n where options are:");
esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=all docgroups; 2=indentation; 80=width */
return 0;
}
do_blosum = esl_opt_GetBoolean(go, "--blosum");
do_gsc = esl_opt_GetBoolean(go, "--gsc");
do_pb = esl_opt_GetBoolean(go, "--pb");
maxid = esl_opt_GetReal (go, "--id");
maxN = esl_opt_GetInteger(go, "--maxN");
if (esl_opt_ArgNumber(go) != 1) {
puts("Incorrect number of command line arguments.");
puts(usage);
return 1;
}
if ((msafile = esl_opt_GetArg(go, 1)) == NULL) esl_fatal("failed to parse cmd line: %s", go->errbuf);
esl_getopts_Destroy(go);
w = esl_stopwatch_Create();
/* Weight one or more alignments from input file
*/
esl_msafile_Open(msafile, eslMSAFILE_UNKNOWN, NULL, &afp);
while (esl_msa_Read(afp, &msa) == eslOK)
{
if (maxN > 0 && msa->nseq > maxN) { esl_msa_Destroy(msa); continue; }
esl_stopwatch_Start(w);
if (do_gsc) esl_msaweight_GSC(msa);
else if (do_pb) esl_msaweight_PB(msa);
else if (do_blosum) esl_msaweight_BLOSUM(msa, maxid);
esl_stopwatch_Stop(w);
cpu = w->user;
printf("%-20s %6d %6d %.3f\n", msa->name, msa->alen, msa->nseq, cpu);
esl_msa_Destroy(msa);
}
esl_msafile_Close(afp);
esl_stopwatch_Destroy(w);
return eslOK;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
ESL_SQ *sq = NULL;
float nullsc, filtersc, H;
int status;
/* Read one HMM from <hmmfile> */
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
p7_hmmfile_Close(hfp);
/* Open <seqfile> for reading */
status = esl_sqfile_OpenDigital(abc, seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) esl_fatal("No such file.");
else if (status == eslEFORMAT) esl_fatal("Format unrecognized.");
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
sq = esl_sq_CreateDigital(abc);
bg = p7_bg_Create(abc);
p7_bg_SetFilter(bg, hmm->M, hmm->compo);
H = esl_vec_FEntropy(bg->f, bg->abc->K);
printf("bg iid H = %.4f\n", H);
H = esl_vec_FEntropy(hmm->compo, bg->abc->K);
printf("modelcomp H = %.4f\n", H);
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
p7_bg_SetLength(bg, sq->n);
p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
p7_bg_FilterScore(bg, sq->dsq, sq->n, &filtersc);
printf("%-20s %5d %8.5f %8.5f %8.5f\n", sq->name, (int) sq->n, nullsc, filtersc, filtersc-nullsc);
esl_sq_Reuse(sq);
}
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s)\n%s\n",
sqfp->filename, sqfp->get_error(sqfp));
else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
status, sqfp->filename);
esl_sqfile_Close(sqfp);
esl_sq_Destroy(sq);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_GMX *gx = NULL;
P7_OMX *fwd = NULL;
P7_TRACE *tr = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float sc, fsc, vsc;
float bestsc = -eslINFINITY;
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc); p7_bg_SetLength(bg, L);
gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL);
om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om);
fwd = p7_omx_Create(gm->M, L, L);
gx = p7_gmx_Create(gm->M, L);
tr = p7_trace_Create();
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_GViterbi(dsq, L, gm, gx, &vsc);
p7_Forward (dsq, L, om, fwd, &fsc);
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
p7_StochasticTrace(r, dsq, L, om, fwd, tr);
p7_trace_Score(tr, dsq, gm, &sc);
bestsc = ESL_MAX(bestsc, sc);
p7_trace_Reuse(tr);
}
esl_stopwatch_Stop(w);
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("forward sc = %.4f nats\n", fsc);
printf("viterbi sc = %.4f nats\n", vsc);
printf("max trace sc = %.4f nats\n", bestsc);
free(dsq);
p7_trace_Destroy(tr);
p7_gmx_Destroy(gx);
p7_omx_Destroy(fwd);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_GMX *gx = NULL;
P7_OMX *fwd = NULL;
P7_OMX *bck = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float fraw, braw, nullsc, fsc;
float gfraw, gbraw, gfsc;
double P, gP;
int status;
/* Read in one HMM */
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
/* Open sequence file for reading */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
/* create default null model, then create and optimize profile */
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, sq->n);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNILOCAL);
om = p7_oprofile_Create(gm->M, abc);
p7_oprofile_Convert(gm, om);
/* p7_oprofile_Dump(stdout, om); */
/* allocate DP matrices for O(M+L) parsers */
fwd = p7_omx_Create(gm->M, 0, sq->n);
bck = p7_omx_Create(gm->M, 0, sq->n);
gx = p7_gmx_Create(gm->M, sq->n);
/* allocate DP matrices for O(ML) fills */
/* fwd = p7_omx_Create(gm->M, sq->n, sq->n); */
/* bck = p7_omx_Create(gm->M, sq->n, sq->n); */
/* p7_omx_SetDumpMode(stdout, fwd, TRUE); */ /* makes the fast DP algorithms dump their matrices */
/* p7_omx_SetDumpMode(stdout, bck, TRUE); */
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
p7_oprofile_ReconfigLength(om, sq->n);
p7_ReconfigLength(gm, sq->n);
p7_bg_SetLength(bg, sq->n);
p7_omx_GrowTo(fwd, om->M, 0, sq->n);
p7_omx_GrowTo(bck, om->M, 0, sq->n);
p7_gmx_GrowTo(gx, gm->M, sq->n);
p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
p7_ForwardParser (sq->dsq, sq->n, om, fwd, &fraw);
p7_BackwardParser(sq->dsq, sq->n, om, fwd, bck, &braw);
/* p7_Forward (sq->dsq, sq->n, om, fwd, &fsc); printf("forward: %.2f nats\n", fsc); */
/* p7_Backward(sq->dsq, sq->n, om, fwd, bck, &bsc); printf("backward: %.2f nats\n", bsc); */
/* Comparison to other F/B implementations */
p7_GForward (sq->dsq, sq->n, gm, gx, &gfraw);
p7_GBackward (sq->dsq, sq->n, gm, gx, &gbraw);
/* p7_gmx_Dump(stdout, gx, p7_DEFAULT); */
fsc = (fraw-nullsc) / eslCONST_LOG2;
gfsc = (gfraw-nullsc) / eslCONST_LOG2;
P = esl_exp_surv(fsc, om->evparam[p7_FTAU], om->evparam[p7_FLAMBDA]);
gP = esl_exp_surv(gfsc, gm->evparam[p7_FTAU], gm->evparam[p7_FLAMBDA]);
if (esl_opt_GetBoolean(go, "-1"))
{
printf("%-30s\t%-20s\t%9.2g\t%6.1f\t%9.2g\t%6.1f\n", sq->name, hmm->name, P, fsc, gP, gfsc);
}
else if (esl_opt_GetBoolean(go, "-P"))
{ /* output suitable for direct use in profmark benchmark postprocessors: */
printf("%g\t%.2f\t%s\t%s\n", P, fsc, sq->name, hmm->name);
}
else
{
printf("target sequence: %s\n", sq->name);
printf("fwd filter raw score: %.2f nats\n", fraw);
printf("bck filter raw score: %.2f nats\n", braw);
printf("null score: %.2f nats\n", nullsc);
printf("per-seq score: %.2f bits\n", fsc);
printf("P-value: %g\n", P);
printf("GForward raw score: %.2f nats\n", gfraw);
printf("GBackward raw score: %.2f nats\n", gbraw);
printf("GForward seq score: %.2f bits\n", gfsc);
printf("GForward P-value: %g\n", gP);
}
esl_sq_Reuse(sq);
}
/* cleanup */
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
p7_omx_Destroy(bck);
p7_omx_Destroy(fwd);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_GMX *gx = NULL;
P7_OMX *fwd = NULL;
P7_OMX *bck = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float fsc, bsc;
float fsc2, bsc2;
double base_time, bench_time, Mcs;
p7_FLogsumInit();
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, L);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
om = p7_oprofile_Create(gm->M, abc);
p7_oprofile_Convert(gm, om);
p7_oprofile_ReconfigLength(om, L);
if (esl_opt_GetBoolean(go, "-x") && p7_FLogsumError(-0.4, -0.5) > 0.0001)
p7_Fail("-x here requires p7_Logsum() recompiled in slow exact mode");
if (esl_opt_GetBoolean(go, "-P")) {
fwd = p7_omx_Create(gm->M, 0, L);
bck = p7_omx_Create(gm->M, 0, L);
} else {
fwd = p7_omx_Create(gm->M, L, L);
bck = p7_omx_Create(gm->M, L, L);
}
gx = p7_gmx_Create(gm->M, L);
/* Get a baseline time: how long it takes just to generate the sequences */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++) esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
esl_stopwatch_Stop(w);
base_time = w->user;
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
if (esl_opt_GetBoolean(go, "-P")) {
if (! esl_opt_GetBoolean(go, "-B")) p7_ForwardParser (dsq, L, om, fwd, &fsc);
if (! esl_opt_GetBoolean(go, "-F")) p7_BackwardParser(dsq, L, om, fwd, bck, &bsc);
} else {
if (! esl_opt_GetBoolean(go, "-B")) p7_Forward (dsq, L, om, fwd, &fsc);
if (! esl_opt_GetBoolean(go, "-F")) p7_Backward(dsq, L, om, fwd, bck, &bsc);
}
if (esl_opt_GetBoolean(go, "-c") || esl_opt_GetBoolean(go, "-x"))
{
p7_GForward (dsq, L, gm, gx, &fsc2);
p7_GBackward(dsq, L, gm, gx, &bsc2);
printf("%.4f %.4f %.4f %.4f\n", fsc, bsc, fsc2, bsc2);
}
}
esl_stopwatch_Stop(w);
bench_time = w->user - base_time;
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_omx_Destroy(bck);
p7_omx_Destroy(fwd);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *seqfile = NULL; /* sequence file name */
char *maskfile = NULL; /* mask coordinate file name */
int infmt = eslSQFILE_UNKNOWN; /* format code for seqfile */
int outfmt = eslSQFILE_FASTA; /* format code for output seqs */
ESL_SQFILE *sqfp = NULL; /* open sequence file */
ESL_FILEPARSER *maskefp = NULL; /* open mask coord file */
FILE *ofp = NULL; /* output stream for masked seqs */
char *source = NULL; /* name of current seq to mask */
char *p1, *p2; /* pointers used in parsing */
int64_t start, end; /* start, end coord for masking */
int64_t i, j, pos; /* coords in a sequence */
int64_t overmask; /* # of extra residues to mask */
ESL_SQ *sq = esl_sq_Create(); /* current sequence */
int do_fetching;
int do_lowercase;
int maskchar;
int status; /* easel return code */
/****************************************************************************
* Parse command line
****************************************************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
do_fetching = esl_opt_GetBoolean(go, "-R");
do_lowercase = esl_opt_GetBoolean(go, "-l");
overmask = (esl_opt_IsOn(go, "-x") ? esl_opt_GetInteger(go, "-x") : 0);
maskchar = (esl_opt_IsOn(go, "-m") ? esl_opt_GetChar(go, "-m") : 'X');
seqfile = esl_opt_GetArg(go, 1);
maskfile = esl_opt_GetArg(go, 2);
/* Open the <seqfile>: text mode, not digital */
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) cmdline_failure(argv[0], "%s is not a valid input sequence file format for --informat");
}
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) cmdline_failure(argv[0], "Sequence file %s not found.\n", seqfile);
else if (status == eslEFORMAT) cmdline_failure(argv[0], "Format of file %s unrecognized.\n", seqfile);
else if (status == eslEINVAL) cmdline_failure(argv[0], "Can't autodetect stdin or .gz.\n");
else if (status != eslOK) cmdline_failure(argv[0], "Open failed, code %d.\n", status);
if (do_fetching && sqfp->data.ascii.ssi == NULL)
cmdline_failure(argv[0], "-R option (random access/fetching) requires %s to be SSI indexed\n", seqfile);
/* Open the <maskfile> */
if (esl_fileparser_Open(maskfile, NULL, &maskefp) != eslOK)
cmdline_failure(argv[0], "Failed to open mask coordinate file %s\n", maskfile);
esl_fileparser_SetCommentChar(maskefp, '#');
/* Open the output file, if any */
if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/****************************************************************************
* Main loop over lines in <maskfile>
****************************************************************************/
/* Read one data line at a time from the <maskfile>;
* parse into data fields <seqname> <start> <end>
*/
while (esl_fileparser_NextLine(maskefp) == eslOK)
{
/* First field is sequence name */
if (esl_fileparser_GetTokenOnLine(maskefp, &source, NULL) != eslOK)
esl_fatal("Failed to read source seq name on line %d of file %s\n", maskefp->linenumber, maskfile);
/* Get the sequence */
if (do_fetching)
{ /* If the <seqfile> is SSI indexed, try to reposition it and read <source> seq by random access */
status = esl_sqio_Fetch(sqfp, source, sq);
if (status == eslENOTFOUND) esl_fatal("seq %s not found in SSI index for file %s\n", source, sqfp->filename);
else if (status == eslEINVAL) esl_fatal("No SSI index or can't reposition in file %s\n", sqfp->filename);
else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslOK) esl_fatal("Unexpected failure in fetching %s from file %s\n", source, sqfp->filename);
}
else
{ /* else, assume we're reading sequentially; <sqfile> and <maskfile> have seqs in same order */
status = esl_sqio_Read(sqfp, sq);
if (status == eslEOF) esl_fatal("File %s ended prematurely; didn't find %s\n", sqfp->filename, source);
else if (status == eslEFORMAT) esl_fatal("Parse failed:\n%s\n", esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslOK) esl_fatal("Unexpected error reading sequence file %s\n", sqfp->filename);
if ((strcmp(sq->name, source) != 0) && (strcmp(sq->acc, source) != 0))
esl_fatal("Sequences in <sqfile> and <maskfile> aren't in same order; try -R");
}
/* If we're masking by lowercase, first make sure everything's uppercase */
if (do_lowercase)
for (pos = 0; pos < sq->n; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = toupper(sq->seq[pos]);
/* Next two fields are <start>, <end> for the masking */
/* possible future extension: wrap loop around this, enable multiple masked regions */
if (esl_fileparser_GetTokenOnLine(maskefp, &p1, NULL) != eslOK)
esl_fatal("Failed to read start coord on line %d of file %s\n", maskefp->linenumber, maskfile);
start = strtoll(p1, &p2, 0) - 1;
if (esl_fileparser_GetTokenOnLine(maskefp, &p2, NULL) != eslOK)
esl_fatal("Failed to read end coord on line %d of file %s\n", maskefp->linenumber, maskfile);
end = strtoll(p2, &p1, 0) - 1;
/* Do the masking */
if (esl_opt_GetBoolean(go, "-r")) /* Reverse masking */
{ /* leave start..end unmasked; mask prefix 0..start-1, end+1..L-1 */
i = 0;
j = ESL_MIN(sq->n-1, start - 1 + overmask);
for (pos = i; pos <= j; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
i = ESL_MAX(0, end + 1 - overmask);
j = sq->n-1;
for (pos = i; pos <= j; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
}
else
{ /* normal: mask start..end */
i = ESL_MAX(0, start - overmask);
j = ESL_MIN(sq->n-1, end + overmask);
for (pos = i; pos <= j; pos++)
if (isalpha(sq->seq[pos]))
sq->seq[pos] = (do_lowercase ? tolower(sq->seq[pos]) : maskchar);
}
esl_sqio_Write(ofp, sq, outfmt, FALSE);
esl_sq_Reuse(sq);
}
esl_sq_Destroy(sq);
esl_fileparser_Close(maskefp);
esl_sqfile_Close(sqfp);
esl_getopts_Destroy(go);
if (ofp != stdout) fclose(ofp);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
char *seqfile = NULL; /* sequence file name */
int infmt = eslSQFILE_UNKNOWN; /* format code for seqfile */
ESL_SQFILE *sqfp = NULL; /* open sequence file */
FILE *ofp = NULL; /* output stream for sequences */
int status; /* easel return code */
/***********************************************
* Parse command line
***********************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) cmdline_failure(argv[0], "Failed to parse command line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) cmdline_failure(argv[0], "Error in configuration: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") ) cmdline_help (argv[0], go);
if (esl_opt_ArgNumber(go) < 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
/* Open the sequence file */
seqfile = esl_opt_GetArg(go, 1);
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) esl_fatal("%s is not a valid input sequence file format for --informat", esl_opt_GetString(go, "--informat"));
}
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) cmdline_failure(argv[0], "Sequence file %s not found.\n", seqfile);
else if (status == eslEFORMAT) cmdline_failure(argv[0], "Format of file %s unrecognized.\n", seqfile);
else if (status == eslEINVAL) cmdline_failure(argv[0], "Can't autodetect stdin or .gz.\n");
else if (status != eslOK) cmdline_failure(argv[0], "Open failed, code %d.\n", status);
/* Open the output file, if any */
if (esl_opt_GetBoolean(go, "-O"))
{
if ((ofp = fopen(esl_opt_GetArg(go, 2), "w")) == NULL)
cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetArg(go, 2));
}
else if (esl_opt_GetString(go, "-o") != NULL)
{
if ((ofp = fopen(esl_opt_GetString(go, "-o"), "w")) == NULL)
cmdline_failure(argv[0], "Failed to open output file %s\n", esl_opt_GetString(go, "-o"));
}
else ofp = stdout;
/* Indexing mode */
if (esl_opt_GetBoolean(go, "--index"))
{
if (esl_opt_ArgNumber(go) != 1) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
if (sqfp->data.ascii.do_gzip) cmdline_failure(argv[0], "Can't index a .gz compressed file");
if (sqfp->data.ascii.do_stdin) cmdline_failure(argv[0], "Can't index a standard input pipe");
create_ssi_index(go, sqfp);
}
/* List retrieval mode */
else if (esl_opt_GetBoolean(go, "-f"))
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
/* Open the SSI index for retrieval */
if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->format))
{
status = esl_sqfile_OpenSSI(sqfp, NULL);
if (status == eslEFORMAT) cmdline_failure(argv[0], "SSI index is in incorrect format\n");
else if (status == eslERANGE) cmdline_failure(argv[0], "SSI index is in 64-bit format and we can't read it\n");
else if (status != eslOK) cmdline_failure(argv[0], "Failed to open SSI index\n");
}
if (esl_opt_GetBoolean(go, "-C")) multifetch_subseq(go, ofp, esl_opt_GetArg(go, 2), sqfp);
else multifetch (go, ofp, esl_opt_GetArg(go, 2), sqfp);
}
/* Single sequence retrieval mode */
else
{
if (esl_opt_ArgNumber(go) != 2) cmdline_failure(argv[0], "Incorrect number of command line arguments.\n");
char *key = esl_opt_GetArg(go, 2);
char *cstring = esl_opt_GetString(go, "-c");
char *newname = esl_opt_GetString(go, "-n");
/* Open the SSI index for retrieval */
if (! sqfp->data.ascii.do_gzip && ! sqfp->data.ascii.do_stdin && ! esl_sqio_IsAlignment(sqfp->format))
{
status = esl_sqfile_OpenSSI(sqfp, NULL);
if (status == eslEFORMAT) cmdline_failure(argv[0], "SSI index is in incorrect format\n");
else if (status == eslERANGE) cmdline_failure(argv[0], "SSI index is in 64-bit format and we can't read it\n");
else if (status != eslOK) cmdline_failure(argv[0], "Failed to open SSI index\n");
}
/* -c: subsequence retrieval; else full sequence retrieval */
if (cstring != NULL)
{
uint32_t start, end;
status = esl_regexp_ParseCoordString(cstring, &start, &end);
if (status == eslESYNTAX) esl_fatal("-c takes arg of subseq coords <from>..<to>; %s not recognized", cstring);
if (status == eslFAIL) esl_fatal("Failed to find <from> or <to> coord in %s", cstring);
onefetch_subseq(go, ofp, sqfp, newname, key, start, end);
if (ofp != stdout) printf("\n\nRetrieved subsequence %s/%d-%d.\n", key, start, end);
}
else
{
onefetch(go, ofp, esl_opt_GetArg(go, 2), sqfp);
if (ofp != stdout) printf("\n\nRetrieved sequence %s.\n", esl_opt_GetArg(go, 2));
}
}
esl_sqfile_Close(sqfp);
esl_getopts_Destroy(go);
return 0;
}
/* seq_shuffling()
* SRE, Tue Jan 22 08:35:51 2008 [Market Street Cafe, Leesburg]
*
* Shuffling of input sequences.
*
* Fixed-length (L>0) vs. full-length (L=0) modes handled differently.
* In fixed-length mode:
* <shuff->seq> only needs to be allocated once, for L
* <targ> is an allocated copy of a random subseq of length L
* sequences < L residues long can't be shuffled
* In full-length mode:
* <shuff->seq> is grown to length <sq->n> for each input seq
* <targ> just points to <sq->seq>
*/
static int
seq_shuffling(ESL_GETOPTS *go, ESL_RANDOMNESS *r, FILE *ofp, int outfmt)
{
char *seqfile = esl_opt_GetArg(go, 1);
int infmt = eslSQFILE_UNKNOWN;
ESL_SQFILE *sqfp = NULL;
ESL_SQ *sq = esl_sq_Create();
ESL_SQ *shuff = esl_sq_Create();
char *targ = NULL;
int N = esl_opt_GetInteger(go, "-N");
int L = esl_opt_GetInteger(go, "-L"); /* L>0 means select random fixed-len subseqs */
int kmers = 0;
int i;
int status;
if (esl_opt_GetString(go, "--informat") != NULL) {
infmt = esl_sqio_EncodeFormat(esl_opt_GetString(go, "--informat"));
if (infmt == eslSQFILE_UNKNOWN) esl_fatal("%s is not a valid input sequence file format for --informat");
}
if (esl_opt_IsOn(go, "-k")) kmers = esl_opt_GetInteger(go, "-k");
status = esl_sqfile_Open(seqfile, infmt, NULL, &sqfp);
if (status == eslENOTFOUND) esl_fatal("No such file %s", seqfile);
else if (status == eslEFORMAT) esl_fatal("Format of seqfile %s unrecognized.", seqfile);
else if (status == eslEINVAL) esl_fatal("Can't autodetect stdin or .gz.");
else if (status != eslOK) esl_fatal("Open failed, code %d.", status);
if (L>0) {
esl_sq_GrowTo(shuff, L);
shuff->n = L;
ESL_ALLOC(targ, sizeof(char) * (L+1));
}
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
if (L == 0) { /* shuffling entire sequence */
esl_sq_GrowTo(shuff, sq->n); /* make sure shuff can hold sq */
shuff->n = sq->n;
targ = sq->seq;
} else {
if (sq->n < L) continue; /* reject seqs < L long */
}
for (i = 0; i < N; i++)
{
if (L > 0) { /* fixed-len mode: copy a random subseq */
int pos = esl_rnd_Roll(r, sq->n - L + 1);
strncpy(targ, sq->seq + pos, L);
targ[L] = '\0';
}
/* Do the requested kind of shuffling */
if (esl_opt_GetBoolean(go, "-m")) esl_rsq_CShuffle (r, targ, shuff->seq); /* monoresidue shuffling */
else if (esl_opt_GetBoolean(go, "-d")) esl_rsq_CShuffleDP (r, targ, shuff->seq); /* diresidue shuffling */
else if (esl_opt_IsOn (go, "-k")) esl_rsq_CShuffleKmers(r, targ, kmers, shuff->seq); /* diresidue shuffling */
else if (esl_opt_GetBoolean(go, "-0")) esl_rsq_CMarkov0 (r, targ, shuff->seq); /* 0th order Markov */
else if (esl_opt_GetBoolean(go, "-1")) esl_rsq_CMarkov1 (r, targ, shuff->seq); /* 1st order Markov */
else if (esl_opt_GetBoolean(go, "-r")) esl_rsq_CReverse ( targ, shuff->seq); /* reverse */
else if (esl_opt_IsOn (go, "-w")) { /* regionally shuffle */
int W= esl_opt_GetInteger(go, "-w"); esl_rsq_CShuffleWindows(r, targ, W, shuff->seq);
}
/* Set the name of the shuffled sequence */
if (N > 1) esl_sq_FormatName(shuff, "%s-shuffled-%d", sq->name, i);
else esl_sq_FormatName(shuff, "%s-shuffled", sq->name);
/* Output the resulting sequence */
esl_sqio_Write(ofp, shuff, outfmt, FALSE);
/* don't need to reuse the shuffled sequence: we will use exactly the same memory */
}
esl_sq_Reuse(sq);
}
if (status == eslEFORMAT) esl_fatal("Parse failed (sequence file %s):\n%s\n",
sqfp->filename, esl_sqfile_GetErrorBuf(sqfp));
else if (status != eslEOF) esl_fatal("Unexpected error %d reading sequence file %s",
status, sqfp->filename);
if (L>0) free(targ);
esl_sq_Destroy(shuff);
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
return eslOK;
ERROR:
if (targ != NULL) free(targ);
esl_sq_Destroy(shuff);
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
return status;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_OMX *fwd = NULL;
P7_OMX *bck = NULL;
P7_OMX *pp = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float fsc, bsc;
double Mcs;
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc); p7_bg_SetLength(bg, L);
gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om);
p7_oprofile_ReconfigLength(om, L);
fwd = p7_omx_Create(gm->M, L, L);
bck = p7_omx_Create(gm->M, L, L);
pp = p7_omx_Create(gm->M, L, L);
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_Forward (dsq, L, om, fwd, &fsc);
p7_Backward(dsq, L, om, fwd, bck, &bsc);
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
p7_Decoding(om, fwd, bck, pp);
esl_stopwatch_Stop(w);
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) w->user;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_omx_Destroy(fwd);
p7_omx_Destroy(bck);
p7_omx_Destroy(pp);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return eslOK;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go;
char *msafile;
ESL_MSAFILE *afp;
ESL_MSA *msa;
int do_gsc;
int do_pb;
int do_blosum;
int maxN;
double maxid;
int nsmall, nbig;
int i;
/* Process command line
*/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) esl_fatal("%s", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) esl_fatal("%s", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") == TRUE){
puts(usage);
puts("\n where options are:");
esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=all docgroups; 2=indentation; 80=width */
return 0;
}
do_blosum = esl_opt_GetBoolean(go, "--blosum");
do_gsc = esl_opt_GetBoolean(go, "--gsc");
do_pb = esl_opt_GetBoolean(go, "--pb");
maxid = esl_opt_GetReal (go, "--id");
maxN = esl_opt_GetInteger(go, "--maxN");
if (esl_opt_ArgNumber(go) != 1) {
puts("Incorrect number of command line arguments.");
puts(usage);
return 1;
}
if ((msafile = esl_opt_GetArg(go, 1)) == NULL) esl_fatal("%s", go->errbuf);
esl_getopts_Destroy(go);
/* Weight one or more alignments from input file
*/
esl_msafile_Open(msafile, eslMSAFILE_UNKNOWN, NULL, &afp);
while (esl_msa_Read(afp, &msa) == eslOK)
{
if (maxN > 0 && msa->nseq > maxN) { esl_msa_Destroy(msa); continue; }
if (do_gsc) esl_msaweight_GSC(msa);
else if (do_pb) esl_msaweight_PB(msa);
else if (do_blosum) esl_msaweight_BLOSUM(msa, maxid);
for (nsmall = 0, nbig = 0, i = 0; i < msa->nseq; i++) {
if (msa->wgt[i] < 0.2) nsmall++;
if (msa->wgt[i] > 5.0) nbig++;
}
printf("%-20s %5d %5d %8.4f %8.4f %5d %5d\n",
msa->name,
msa->nseq,
msa->alen,
esl_vec_DMin(msa->wgt, msa->nseq),
esl_vec_DMax(msa->wgt, msa->nseq),
nsmall,
nbig);
esl_msa_Destroy(msa);
}
esl_msafile_Close(afp);
return eslOK;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_GMX *fwd = NULL;
P7_GMX *bck = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float sc;
double base_time, bench_time, Mcs;
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, L);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, L, p7_UNILOCAL);
fwd = p7_gmx_Create(gm->M, L);
bck = p7_gmx_Create(gm->M, L);
/* Baseline time. */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++) esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
esl_stopwatch_Stop(w);
base_time = w->user;
/* Benchmark time. */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
if (! esl_opt_GetBoolean(go, "-B")) p7_GForward (dsq, L, gm, fwd, &sc);
if (! esl_opt_GetBoolean(go, "-F")) p7_GBackward(dsq, L, gm, bck, NULL);
}
esl_stopwatch_Stop(w);
bench_time = w->user - base_time;
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_gmx_Destroy(bck);
p7_gmx_Destroy(fwd);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
int status;
ESL_GETOPTS *go = NULL; /* command line processing */
ESL_ALPHABET *abc = NULL;
char *hmmfile = NULL;
char *outhmmfile = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
int nhmm;
double x;
float KL;
char errmsg[eslERRBUFSIZE];
/* Process the command line options.
*/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK ||
esl_opt_VerifyConfig(go) != eslOK)
{
printf("Failed to parse command line: %s\n", go->errbuf);
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
if (esl_opt_GetBoolean(go, "-h") == TRUE)
{
profillic_p7_banner(stdout, argv[0], banner);
esl_usage(stdout, argv[0], usage);
puts("\nwhere options are:");
esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=docgroup, 2 = indentation; 80=textwidth*/
exit(0);
}
if (esl_opt_ArgNumber(go) != 2)
{
puts("Incorrect number of command line arguments.");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
if ((hmmfile = esl_opt_GetArg(go, 1)) == NULL)
{
puts("Failed to read <input hmmfile> argument from command line.");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
if ((outhmmfile = esl_opt_GetArg(go, 2)) == NULL)
{
puts("Failed to read <output hmmfile> argument from command line.");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
profillic_p7_banner(stdout, argv[0], banner);
/* Initializations: open the input HMM file for reading
*/
status = p7_hmmfile_Open(hmmfile, NULL, &hfp);
if (status == eslENOTFOUND) p7_Fail("Failed to open HMM file %s for reading.\n", hmmfile);
else if (status == eslEFORMAT) p7_Fail("File %s does not appear to be in a recognized HMM format.\n", hmmfile);
else if (status != eslOK) p7_Fail("Unexpected error %d in opening HMM file %s.\n", status, hmmfile);
/* Main body: read HMMs one at a time, print one line of stats
*/
printf("#\n");
printf("# %-4s %-20s %-12s %8s %8s %6s %6s %6s %6s %6s\n", "idx", "name", "accession", "nseq", "eff_nseq", "M", "relent", "info", "p relE", "compKL");
printf("# %-4s %-20s %-12s %8s %8s %6s %6s %6s %6s %6s\n", "----", "--------------------", "------------", "--------", "--------", "------", "------", "------", "------", "------");
nhmm = 0;
if ((status = p7_hmmfile_Read(hfp, &abc, &hmm)) != eslEOF)
{
if (status == eslEOD) esl_fatal("read failed, HMM file %s may be truncated?", hmmfile);
else if (status == eslEFORMAT) esl_fatal("bad file format in HMM file %s", hmmfile);
else if (status == eslEINCOMPAT) esl_fatal("HMM file %s contains different alphabets", hmmfile);
else if (status != eslOK) esl_fatal("Unexpected error in reading HMMs from %s", hmmfile);
nhmm++;
if (bg == NULL) bg = p7_bg_Create(abc);
if( abc->type == eslDNA ) {
galosh::ProfileTreeRoot<seqan::Dna, floatrealspace> profile;
if( (status = convert_to_galosh_profile( hmm, profile )) != eslOK ) esl_fatal("Unexpected error in converting HMM from file %s to a dna galosh profile", hmmfile);
std::ofstream fs ( outhmmfile );
if( !fs.is_open() ) {
esl_fatal("Unexpected error in opening the file %s for writing", outhmmfile);
} else {
fs << profile;
fs.close();
}
} else if( abc->type == eslAMINO ) {
galosh::ProfileTreeRoot<seqan::AminoAcid20, floatrealspace> profile;
if( (status = convert_to_galosh_profile( hmm, profile )) != eslOK ) esl_fatal("Unexpected error in converting HMM from file %s to an amino galosh profile", hmmfile);
std::ofstream fs ( outhmmfile );
if( !fs.is_open() ) {
esl_fatal("Unexpected error in opening the file %s for writing", outhmmfile);
} else {
fs << profile;
fs.close();
}
} else {
ESL_EXCEPTION(eslEUNIMPLEMENTED, "Sorry, at present the profillic-hmmtoprofile software can only handle amino and dna.");
}
p7_MeanPositionRelativeEntropy(hmm, bg, &x);
p7_hmm_CompositionKLDist(hmm, bg, &KL, NULL);
printf("%-6d %-20s %-12s %8d %8.2f %6d %6.2f %6.2f %6.2f %6.2f\n",
nhmm,
hmm->name,
hmm->acc == NULL ? "-" : hmm->acc,
hmm->nseq,
hmm->eff_nseq,
hmm->M,
p7_MeanMatchRelativeEntropy(hmm, bg),
p7_MeanMatchInfo(hmm, bg),
x,
KL);
/* p7_MeanForwardScore(hmm, bg)); */
p7_hmm_Destroy(hmm);
}
p7_bg_Destroy(bg);
esl_alphabet_Destroy(abc);
p7_hmmfile_Close(hfp);
esl_getopts_Destroy(go);
exit(0);
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_GMX *fwd = NULL;
P7_GMX *bck = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float fsc, bsc;
int status;
/* Read in one HMM */
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
p7_hmmfile_Close(hfp);
/* Read in one sequence */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
if (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");
esl_sqfile_Close(sqfp);
/* Configure a profile from the HMM */
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, sq->n);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNILOCAL);
/* Allocate matrices */
fwd = p7_gmx_Create(gm->M, sq->n);
bck = p7_gmx_Create(gm->M, sq->n);
/* Run Forward, Backward */
p7_GForward (sq->dsq, sq->n, gm, fwd, &fsc);
p7_GBackward(sq->dsq, sq->n, gm, bck, &bsc);
printf("fwd = %.4f nats\n", fsc);
printf("bck = %.4f nats\n", bsc);
/* Cleanup */
esl_sq_Destroy(sq);
p7_gmx_Destroy(fwd);
p7_gmx_Destroy(bck);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_GMX *fwd = NULL;
P7_GMX *bck = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float fsc, bsc;
float nullsc;
int status;
/* Initialize log-sum calculator */
p7_FLogsumInit();
/* Read in one HMM */
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
p7_hmmfile_Close(hfp);
/* Read in one sequence */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
/* Configure a profile from the HMM */
bg = p7_bg_Create(abc);
gm = p7_profile_Create(hmm->M, abc);
/* Now reconfig the models however we were asked to */
if (esl_opt_GetBoolean(go, "--fs")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
else if (esl_opt_GetBoolean(go, "--sw")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNILOCAL);
else if (esl_opt_GetBoolean(go, "--ls")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_GLOCAL);
else if (esl_opt_GetBoolean(go, "--s")) p7_ProfileConfig(hmm, bg, gm, sq->n, p7_UNIGLOCAL);
/* Allocate matrices */
fwd = p7_gmx_Create(gm->M, sq->n);
bck = p7_gmx_Create(gm->M, sq->n);
printf("%-30s %-10s %-10s %-10s %-10s\n", "# seq name", "fwd (raw)", "bck (raw) ", "fwd (bits)", "bck (bits)");
printf("%-30s %10s %10s %10s %10s\n", "#--------------", "----------", "----------", "----------", "----------");
while ( (status = esl_sqio_Read(sqfp, sq)) != eslEOF)
{
if (status == eslEFORMAT) p7_Fail("Parse failed (sequence file %s)\n%s\n", sqfp->filename, sqfp->get_error(sqfp));
else if (status != eslOK) p7_Fail("Unexpected error %d reading sequence file %s", status, sqfp->filename);
/* Resize the DP matrices if necessary */
p7_gmx_GrowTo(fwd, gm->M, sq->n);
p7_gmx_GrowTo(bck, gm->M, sq->n);
/* Set the profile and null model's target length models */
p7_bg_SetLength(bg, sq->n);
p7_ReconfigLength(gm, sq->n);
/* Run Forward, Backward */
p7_GForward (sq->dsq, sq->n, gm, fwd, &fsc);
p7_GBackward(sq->dsq, sq->n, gm, bck, &bsc);
p7_gmx_Dump(stdout, fwd, p7_DEFAULT);
/* Those scores are partial log-odds likelihoods in nats.
* Subtract off the rest of the null model, convert to bits.
*/
p7_bg_NullOne(bg, sq->dsq, sq->n, &nullsc);
printf("%-30s %10.4f %10.4f %10.4f %10.4f\n",
sq->name,
fsc, bsc,
(fsc - nullsc) / eslCONST_LOG2, (bsc - nullsc) / eslCONST_LOG2);
p7_gmx_Reuse(fwd);
p7_gmx_Reuse(bck);
esl_sq_Reuse(sq);
}
/* Cleanup */
esl_sqfile_Close(sqfp);
esl_sq_Destroy(sq);
p7_gmx_Destroy(fwd);
p7_gmx_Destroy(bck);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = NULL; /* application configuration */
ESL_ALPHABET *abc = NULL; /* biological alphabet */
char *alifile = NULL; /* alignment file name */
int fmt = eslMSAFILE_UNKNOWN; /* format code for alifile */
ESLX_MSAFILE *afp = NULL; /* open msa file */
ESL_MSAFILE2 *old_afp = NULL; /* open msa file, legacy (--small) */
ESL_MSA *msa = NULL; /* one multiple sequence alignment */
int nali; /* number of alignments read */
int i; /* counter over seqs */
int64_t alen; /* alignment length */
int nseq; /* number of sequences in the msa */
int64_t rlen; /* a raw (unaligned) seq length */
int64_t small, large; /* smallest, largest sequence */
int64_t nres; /* total # of residues in msa */
double avgid; /* average fractional pair id */
int max_comparisons; /* maximum # comparisons for avg id */
int do_stall; /* used to stall when debugging */
double **abc_ct = NULL; /* [0..msa->alen-1][0..abc->K] number of each residue at each position (abc->K is gap) */
double ***bp_ct = NULL; /* [0..msa->alen-1][0..abc->Kp-1][0..abc->Kp-1] per (non-pknotted) consensus basepair *
* count of each possible basepair over all seqs basepairs are indexed by 'i' the minimum *
* of 'i:j' for a pair between i and j, where i < j. */
double **pp_ct = NULL; /* [0..msa->alen-1][0..11], count of each posterior probability (PP) code, over all sequences, gap is 11 */
int *i_am_rf = NULL; /* [0..i..msa->alen-1]: TRUE if pos i is non-gap RF posn, if msa->rf == NULL remains NULL */
int *rf2a_map = NULL; /* [0..rfpos..rflen-1] = apos,
* apos is the alignment position (0..msa->alen-1) that
* is non-gap RF position rfpos+1 (for rfpos in 0..rflen-1) */
int rflen = -1; /* nongap RF length */
char errbuf[eslERRBUFSIZE];
int status; /* easel return code */
/* optional output files */
FILE *iinfofp = NULL; /* output file for --iinfo */
FILE *pcinfofp = NULL; /* output file for --pcinfo */
FILE *psinfofp = NULL; /* output file for --psinfo */
FILE *rinfofp = NULL; /* output file for --rinfo */
FILE *icinfofp = NULL; /* output file for --icinfo */
FILE *listfp = NULL; /* output file for --list */
FILE *cinfofp = NULL; /* output file for --cinfo */
FILE *bpinfofp = NULL; /* output file for --bpinfo */
int use_weights; /* TRUE if --weight, reported weighted counts (using msa->wgt) to all output files */
int weights_exist; /* TRUE if at least one msa->wgt value differs from 1.0, FALSE if not (or if msa->wgt==NULL) */
/***********************************************
* Parse command line
***********************************************/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK ||
esl_opt_VerifyConfig(go) != eslOK)
{
printf("Failed to parse command line: %s\n", go->errbuf);
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
if (esl_opt_GetBoolean(go, "-h") )
{
esl_banner(stdout, argv[0], banner);
esl_usage (stdout, argv[0], usage);
puts("\n where options are:");
esl_opt_DisplayHelp(stdout, go, 1, 2, 80);
puts("\n small memory mode, requires --amino,--dna, or --rna and --informat pfam:");
esl_opt_DisplayHelp(stdout, go, 2, 2, 80);
puts("\n optional output files:");
esl_opt_DisplayHelp(stdout, go, 3, 2, 80);
exit(0);
}
if (esl_opt_ArgNumber(go) != 1)
{
printf("Incorrect number of command line arguments.\n");
esl_usage(stdout, argv[0], usage);
printf("\nTo see more help on available options, do %s -h\n\n", argv[0]);
exit(1);
}
alifile = esl_opt_GetArg(go, 1);
if (esl_opt_IsOn(go, "--informat") &&
(fmt = eslx_msafile_EncodeFormat(esl_opt_GetString(go, "--informat"))) == eslMSAFILE_UNKNOWN)
esl_fatal("%s is not a valid input sequence file format for --informat", esl_opt_GetString(go, "--informat"));
if (esl_opt_GetBoolean(go, "--small") && fmt != eslMSAFILE_PFAM) esl_fatal("--small requires --informat pfam\n");
max_comparisons = 1000;
do_stall = esl_opt_GetBoolean(go, "--stall"); /* a stall point for attaching gdb */
while (do_stall);
/***********************************************
* Open the MSA file; determine alphabet; set for digital input
***********************************************/
if (esl_opt_GetBoolean(go, "--amino")) abc = esl_alphabet_Create(eslAMINO);
else if (esl_opt_GetBoolean(go, "--dna")) abc = esl_alphabet_Create(eslDNA);
else if (esl_opt_GetBoolean(go, "--rna")) abc = esl_alphabet_Create(eslRNA);
/* We'd like to get rid of the legacy msafile interface, but it
* includes small memory functionality for Pfam format which we have
* to replace first. For now, use both interfaces, new and legacy
*/
if ( esl_opt_GetBoolean(go, "--small") )
{
if (! abc) esl_fatal("--small requires one of --amino, --dna, --rna be specified.");
status = esl_msafile2_OpenDigital(abc, alifile, NULL, &old_afp);
if (status == eslENOTFOUND) esl_fatal("Alignment file %s doesn't exist or is not readable\n", alifile);
else if (status == eslEFORMAT) esl_fatal("Couldn't determine format of alignment %s\n", alifile);
else if (status != eslOK) esl_fatal("Alignment file open failed with error %d\n", status);
}
else
{
if ( (status = eslx_msafile_Open(&abc, alifile, NULL, fmt, NULL, &afp)) != eslOK)
eslx_msafile_OpenFailure(afp, status);
}
/**************************************
* Open optional output files, as nec *
**************************************/
/* determine name for first list file, if nec */
if( esl_opt_IsOn(go, "--list")) {
if ((listfp = fopen(esl_opt_GetString(go, "--list"), "w")) == NULL)
esl_fatal("Failed to open --list output file %s\n", esl_opt_GetString(go, "--list"));
}
if( esl_opt_IsOn(go, "--icinfo")) {
if ((icinfofp = fopen(esl_opt_GetString(go, "--icinfo"), "w")) == NULL)
esl_fatal("Failed to open --icinfo output file %s\n", esl_opt_GetString(go, "--icinfo"));
}
if( esl_opt_IsOn(go, "--rinfo")) {
if ((rinfofp = fopen(esl_opt_GetString(go, "--rinfo"), "w")) == NULL)
esl_fatal("Failed to open --rinfo output file %s\n", esl_opt_GetString(go, "--rinfo"));
}
if( esl_opt_IsOn(go, "--pcinfo")) {
if ((pcinfofp = fopen(esl_opt_GetString(go, "--pcinfo"), "w")) == NULL)
esl_fatal("Failed to open --pcinfo output file %s\n", esl_opt_GetString(go, "--pcinfo"));
}
if( esl_opt_IsOn(go, "--psinfo")) {
if ((psinfofp = fopen(esl_opt_GetString(go, "--psinfo"), "w")) == NULL)
esl_fatal("Failed to open --psinfo output file %s\n", esl_opt_GetString(go, "--psinfo"));
}
if( esl_opt_IsOn(go, "--iinfo")) {
if ((iinfofp = fopen(esl_opt_GetString(go, "--iinfo"), "w")) == NULL)
esl_fatal("Failed to open --iinfo output file %s\n", esl_opt_GetString(go, "--iinfo"));
}
if( esl_opt_IsOn(go, "--cinfo")) {
if ((cinfofp = fopen(esl_opt_GetString(go, "--cinfo"), "w")) == NULL)
esl_fatal("Failed to open --cinfo output file %s\n", esl_opt_GetString(go, "--cinfo"));
}
if( esl_opt_IsOn(go, "--bpinfo")) {
if ((bpinfofp = fopen(esl_opt_GetString(go, "--bpinfo"), "w")) == NULL)
esl_fatal("Failed to open --bpinfo output file %s\n", esl_opt_GetString(go, "--bpinfo"));
}
/***********************************************
* Read MSAs one at a time.
***********************************************/
if (esl_opt_GetBoolean(go, "-1")) {
puts("#");
if(! esl_opt_GetBoolean(go, "--small")) {
printf("# %-4s %-20s %10s %7s %7s %12s %6s %6s %10s %3s\n", "idx", "name", "format", "nseq", "alen", "nres", "small", "large", "avlen", "%id");
printf("# %-4s %-20s %10s %7s %7s %12s %6s %6s %10s %3s\n", "----", "--------------------", "----------", "-------", "-------", "------------", "------", "------", "----------", "---");
}
else {
printf("# %-4s %-20s %10s %7s %7s %12s %10s\n", "idx", "name", "format", "nseq", "alen", "nres", "avlen");
printf("# %-4s %-20s %10s %7s %7s %12s %10s\n", "----", "--------------------", "----------", "-------", "-------", "------------", "----------");
}
}
nali = 0;
fmt = (esl_opt_GetBoolean(go, "--small") ? old_afp->format : afp->format);
while ( (status = ( esl_opt_GetBoolean(go, "--small") ?
esl_msafile2_ReadInfoPfam(old_afp, listfp, abc, -1, NULL, NULL, &msa, &nseq, &alen, NULL, NULL, NULL, NULL, NULL, &abc_ct, &pp_ct, NULL, NULL, NULL) :
eslx_msafile_Read (afp, &msa))) == eslOK)
{
nali++;
nres = 0;
if (! esl_opt_GetBoolean(go, "--small")) {
nseq = msa->nseq;
alen = msa->alen;
small = large = -1;
for (i = 0; i < msa->nseq; i++)
{
rlen = esl_abc_dsqrlen(msa->abc, msa->ax[i]);
nres += rlen;
if (small == -1 || rlen < small) small = rlen;
if (large == -1 || rlen > large) large = rlen;
}
esl_dst_XAverageId(abc, msa->ax, msa->nseq, max_comparisons, &avgid);
}
else { /* --small invoked */
for(i = 0; i < alen; i++) nres += (int) esl_vec_DSum(abc_ct[i], abc->K);
}
if (esl_opt_GetBoolean(go, "-1"))
{
printf("%-6d %-20s %10s %7d %7" PRId64 " %12" PRId64,
nali,
msa->name,
eslx_msafile_DecodeFormat(fmt),
nseq,
alen,
nres);
if (! esl_opt_GetBoolean(go, "--small")) {
printf(" %6" PRId64 " %6" PRId64 " %10.1f %3.0f\n",
small,
large,
(double) nres / (double) msa->nseq,
100.*avgid);
}
else {
printf(" %10.1f\n", (double) nres / (double) nseq);
}
}
else
{
printf("Alignment number: %d\n", nali);
if (msa->name != NULL)
printf("Alignment name: %s\n", msa->name);
printf("Format: %s\n", eslx_msafile_DecodeFormat(fmt));
printf("Number of sequences: %d\n", nseq);
printf("Alignment length: %" PRId64 "\n", alen);
printf("Total # residues: %" PRId64 "\n", nres);
if(! esl_opt_GetBoolean(go, "--small")) {
printf("Smallest: %" PRId64 "\n", small);
printf("Largest: %" PRId64 "\n", large);
}
printf("Average length: %.1f\n", (double) nres / (double) nseq);
if(! esl_opt_GetBoolean(go, "--small")) {
printf("Average identity: %.0f%%\n", 100.*avgid);
}
printf("//\n");
}
/* Dump data to optional output files, if nec */
if(esl_opt_IsOn(go, "--list")) {
if(! esl_opt_GetBoolean(go, "--small")) {
/* only print sequence name to list file if ! --small, else we already have in esl_msafile2_ReadInfoPfam() */
for(i = 0; i < msa->nseq; i++) fprintf(listfp, "%s\n", msa->sqname[i]);
}
}
/* if RF exists, get i_am_rf array[0..alen] which tells us which positions are non-gap RF positions
* and rf2a_map, a map of non-gap RF positions to overall alignment positions */
if(msa->rf != NULL) {
if((status = map_rfpos_to_apos(msa, abc, errbuf, alen, &i_am_rf, &rf2a_map, &rflen)) != eslOK) esl_fatal(errbuf);
}
else i_am_rf = NULL;
weights_exist = check_msa_weights(msa);
use_weights = (weights_exist && esl_opt_GetBoolean(go, "--weight")) ? TRUE : FALSE;
if( (! esl_opt_GetBoolean(go, "--small")) &&
(esl_opt_IsOn(go, "--icinfo") || esl_opt_IsOn(go, "--rinfo") || esl_opt_IsOn(go, "--pcinfo") ||
esl_opt_IsOn(go, "--cinfo") || esl_opt_IsOn(go, "--bpinfo"))) {
/* collect counts of each residue and PPs (if they exist) from the msa */
if(esl_opt_GetBoolean(go, "--weight") && msa->wgt == NULL) esl_fatal("--weight requires all alignments have #=GS WT annotation, but aln %d does not", nali);
if((status = count_msa(msa, errbuf, nali,
esl_opt_GetBoolean(go, "--noambig"), /* ignore ambiguous residues? */
esl_opt_GetBoolean(go, "--weight"), /* use msa->wgt sequence weights? */
&abc_ct,
((bpinfofp != NULL && msa->ss_cons != NULL) ? &bp_ct : NULL), /* get basepair counts? */
(msa->pp != NULL ? &pp_ct : NULL))) /* get PP counts? */
!= eslOK) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--icinfo")) {
if((status = dump_infocontent_info(icinfofp, abc, abc_ct, use_weights, nali, alen, nseq, i_am_rf, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--rinfo")) {
if((status = dump_residue_info(rinfofp, abc, abc_ct, use_weights, nali, alen, nseq, i_am_rf, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if(esl_opt_IsOn(go, "--pcinfo")) {
if(pp_ct == NULL) esl_fatal("Error: --pcinfo requires all alignments have #=GR PP annotation, but alignment %d does not", nali);
if((status = dump_posterior_column_info(pcinfofp, pp_ct, use_weights, nali, alen, nseq, i_am_rf, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if(esl_opt_IsOn(go, "--psinfo")) {
if(msa->pp == NULL) esl_fatal("Error: --psinfo requires all alignments have #=GR PP annotation, but alignment %d does not", nali);
if((status = dump_posterior_sequence_info(psinfofp, msa, nali, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--iinfo")) {
if(msa->rf == NULL) esl_fatal("--iinfo requires all alignments have #=GC RF annotation, but alignment %d does not", nali);
if(esl_opt_GetBoolean(go, "--weight") && msa->wgt == NULL) esl_fatal("--weight requires all alignments have #=GS WT annotation, but aln %d does not", nali);
if((status = dump_insert_info(iinfofp, msa, use_weights, nali, i_am_rf, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--cinfo")) {
if((status = dump_column_residue_counts(cinfofp, abc, abc_ct, esl_opt_GetBoolean(go, "--noambig"), use_weights, nali, alen, nseq, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
if( esl_opt_IsOn(go, "--bpinfo")) {
if(msa->ss_cons == NULL) esl_fatal("--bpinfo requires all alignments have #=GC SS_cons annotation, but alignment %d does not", nali);
if((status = dump_basepair_counts(bpinfofp, msa, abc, bp_ct, use_weights, nali, nseq, msa->name, alifile, errbuf) != eslOK)) esl_fatal(errbuf);
}
esl_msa_Destroy(msa);
if(abc_ct != NULL) { esl_Free2D((void **) abc_ct, alen); abc_ct = NULL; }
if(bp_ct != NULL) { esl_Free3D((void ***) bp_ct, alen, abc->Kp); bp_ct = NULL; }
if(pp_ct != NULL) { esl_Free2D((void **) pp_ct, alen); pp_ct = NULL; }
if(i_am_rf != NULL) { free(i_am_rf); i_am_rf = NULL; }
if(rf2a_map != NULL) { free(rf2a_map); rf2a_map = NULL; }
}
/* If an msa read failed, we've dropped out to here with an informative status code.
* we have to handle failures from new vs. legacy msa parsing differently
*/
if (esl_opt_GetBoolean(go, "--small"))
{
if (status == eslEFORMAT) esl_fatal("Alignment file parse error, line %d of file %s:\n%s\nOffending line is:\n%s\n", old_afp->linenumber, old_afp->fname, old_afp->errbuf, old_afp->buf);
else if (status != eslEOF) esl_fatal("Alignment file read failed with error code %d\n", status);
else if (nali == 0) esl_fatal("No alignments found in file %s\n", alifile);
}
else
{
if (nali == 0 || status != eslEOF) eslx_msafile_ReadFailure(afp, status);
}
/* Cleanup, normal return
*/
if(listfp != NULL) {
fclose(listfp);
printf("# List of sequences in %d alignment(s) saved to file %s\n", nali, esl_opt_GetString(go, "--list"));
}
if(icinfofp != NULL) {
fclose(icinfofp);
printf("# Information content data saved to file %s.\n", esl_opt_GetString(go, "--icinfo"));
}
if(rinfofp != NULL) {
fclose(rinfofp);
printf("# Residue data saved to file %s.\n", esl_opt_GetString(go, "--rinfo"));
}
if(pcinfofp != NULL) {
fclose(pcinfofp);
printf("# Per-column posterior probability data saved to file %s.\n", esl_opt_GetString(go, "--pcinfo"));
}
if(psinfofp != NULL) {
fclose(psinfofp);
printf("# Per-sequence posterior probability data saved to file %s.\n", esl_opt_GetString(go, "--psinfo"));
}
if(iinfofp != NULL) {
printf("# Insert data saved to file %s.\n", esl_opt_GetString(go, "--iinfo"));
fclose(iinfofp);
}
if(cinfofp != NULL) {
printf("# Per-column counts data saved to file %s.\n", esl_opt_GetString(go, "--cinfo"));
fclose(cinfofp);
}
if(bpinfofp != NULL) {
printf("# Per-column basepair counts data saved to file %s.\n", esl_opt_GetString(go, "--bpinfo"));
fclose(bpinfofp);
}
if (afp) eslx_msafile_Close(afp);
if (old_afp) esl_msafile2_Close(old_afp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 1, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
ESL_STOPWATCH *w = esl_stopwatch_Create();
ESL_RANDOMNESS *r = esl_randomness_CreateFast(esl_opt_GetInteger(go, "-s"));
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_OMX *ox = NULL;
P7_GMX *gx = NULL;
int L = esl_opt_GetInteger(go, "-L");
int N = esl_opt_GetInteger(go, "-N");
ESL_DSQ *dsq = malloc(sizeof(ESL_DSQ) * (L+2));
int i;
float sc1, sc2;
double base_time, bench_time, Mcs;
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, L);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, L, p7_LOCAL);
om = p7_oprofile_Create(gm->M, abc);
p7_oprofile_Convert(gm, om);
p7_oprofile_ReconfigLength(om, L);
if (esl_opt_GetBoolean(go, "-x")) p7_profile_SameAsMF(om, gm);
ox = p7_omx_Create(gm->M, 0, 0);
gx = p7_gmx_Create(gm->M, L);
/* Get a baseline time: how long it takes just to generate the sequences */
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
esl_stopwatch_Stop(w);
base_time = w->user;
esl_stopwatch_Start(w);
for (i = 0; i < N; i++)
{
esl_rsq_xfIID(r, bg->f, abc->K, L, dsq);
p7_MSVFilter (dsq, L, om, ox, &sc1);
/* -c option: compare generic to fast score */
if (esl_opt_GetBoolean(go, "-c"))
{
p7_GMSV (dsq, L, gm, gx, 2.0, &sc2);
printf("%.4f %.4f\n", sc1, sc2);
}
/* -x option: compare generic to fast score in a way that should give exactly the same result */
if (esl_opt_GetBoolean(go, "-x"))
{
p7_GViterbi(dsq, L, gm, gx, &sc2);
sc2 /= om->scale_b;
if (om->mode == p7_UNILOCAL) sc2 -= 2.0; /* that's ~ L \log \frac{L}{L+2}, for our NN,CC,JJ */
else if (om->mode == p7_LOCAL) sc2 -= 3.0; /* that's ~ L \log \frac{L}{L+3}, for our NN,CC,JJ */
printf("%.4f %.4f\n", sc1, sc2);
}
}
esl_stopwatch_Stop(w);
bench_time = w->user - base_time;
Mcs = (double) N * (double) L * (double) gm->M * 1e-6 / (double) bench_time;
esl_stopwatch_Display(stdout, w, "# CPU time: ");
printf("# M = %d\n", gm->M);
printf("# %.1f Mc/s\n", Mcs);
free(dsq);
p7_omx_Destroy(ox);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_stopwatch_Destroy(w);
esl_randomness_Destroy(r);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = esl_getopts_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
ESL_RANDOMNESS *rng = esl_randomness_CreateFast(0);
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_GMX *gx = NULL;
P7_OMX *fwd = NULL;
P7_TRACE *tr = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
int N = esl_opt_GetInteger(go, "-N");
int i;
float vsc, fsc, tsc;
char errbuf[eslERRBUFSIZE];
int status;
/* Read in one HMM */
if (p7_hmmfile_Open(hmmfile, NULL, &hfp) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
/* Read in one sequence */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
if (esl_sqio_Read(sqfp, sq) != eslOK) p7_Fail("Failed to read sequence");
/* create default null model, then create and optimize profile */
bg = p7_bg_Create(abc); p7_bg_SetLength(bg, sq->n);
gm = p7_profile_Create(hmm->M, abc); p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
om = p7_oprofile_Create(gm->M, abc); p7_oprofile_Convert(gm, om);
if (esl_opt_GetBoolean(go, "-p")) p7_oprofile_Dump(stdout, om);
fwd = p7_omx_Create(gm->M, sq->n, sq->n);
gx = p7_gmx_Create(gm->M, sq->n);
tr = p7_trace_Create();
if (esl_opt_GetBoolean(go, "-m") == TRUE) p7_omx_SetDumpMode(stdout, fwd, TRUE);
p7_GViterbi(sq->dsq, sq->n, gm, gx, &vsc);
p7_Forward (sq->dsq, sq->n, om, fwd, &fsc);
for (i = 0; i < N; i++)
{
p7_StochasticTrace(rng, sq->dsq, sq->n, om, fwd, tr);
p7_trace_Score(tr, sq->dsq, gm, &tsc);
if (esl_opt_GetBoolean(go, "-t") == TRUE) p7_trace_Dump(stdout, tr, gm, sq->dsq);
if (p7_trace_Validate(tr, abc, sq->dsq, errbuf) != eslOK) p7_Die("trace %d fails validation:\n%s\n", i, errbuf);
printf("Sampled trace: %.4f nats\n", tsc);
p7_trace_Reuse(tr);
}
printf("Forward score: %.4f nats\n", fsc);
printf("Viterbi score: %.4f nats\n", vsc);
/* cleanup */
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
p7_trace_Destroy(tr);
p7_omx_Destroy(fwd);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_randomness_Destroy(rng);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go = p7_CreateDefaultApp(options, 2, argc, argv, banner, usage);
char *hmmfile = esl_opt_GetArg(go, 1);
char *seqfile = esl_opt_GetArg(go, 2);
ESL_ALPHABET *abc = NULL;
P7_HMMFILE *hfp = NULL;
P7_HMM *hmm = NULL;
P7_BG *bg = NULL;
P7_PROFILE *gm = NULL;
P7_OPROFILE *om = NULL;
P7_OMX *ox = NULL;
P7_GMX *gx = NULL;
ESL_SQ *sq = NULL;
ESL_SQFILE *sqfp = NULL;
int format = eslSQFILE_UNKNOWN;
float msvraw, nullsc, msvscore;
float graw, gscore;
double P, gP;
int status;
/* Read in one HMM */
if (p7_hmmfile_OpenE(hmmfile, NULL, &hfp, NULL) != eslOK) p7_Fail("Failed to open HMM file %s", hmmfile);
if (p7_hmmfile_Read(hfp, &abc, &hmm) != eslOK) p7_Fail("Failed to read HMM");
/* Open sequence file for reading */
sq = esl_sq_CreateDigital(abc);
status = esl_sqfile_Open(seqfile, format, NULL, &sqfp);
if (status == eslENOTFOUND) p7_Fail("No such file.");
else if (status == eslEFORMAT) p7_Fail("Format unrecognized.");
else if (status == eslEINVAL) p7_Fail("Can't autodetect stdin or .gz.");
else if (status != eslOK) p7_Fail("Open failed, code %d.", status);
/* create default null model, then create and optimize profile */
bg = p7_bg_Create(abc);
p7_bg_SetLength(bg, sq->n);
gm = p7_profile_Create(hmm->M, abc);
p7_ProfileConfig(hmm, bg, gm, sq->n, p7_LOCAL);
om = p7_oprofile_Create(gm->M, abc);
p7_oprofile_Convert(gm, om);
/* allocate DP matrices, both a generic and an optimized one */
ox = p7_omx_Create(gm->M, 0, 0); /* one row version */
gx = p7_gmx_Create(gm->M, sq->n);
/* Useful to place and compile in for debugging:
p7_oprofile_Dump(stdout, om); dumps the optimized profile
p7_omx_SetDumpMode(stdout, ox, TRUE); makes the fast DP algorithms dump their matrices
p7_gmx_Dump(stdout, gx, p7_DEFAULT); dumps a generic DP matrix
p7_oprofile_SameMSV(om, gm);
*/
p7_omx_SetDumpMode(stdout, ox, TRUE);
while ((status = esl_sqio_Read(sqfp, sq)) == eslOK)
{
p7_oprofile_ReconfigLength(om, sq->n);
p7_ReconfigLength(gm, sq->n);
p7_bg_SetLength(bg, sq->n);
p7_omx_GrowTo(ox, om->M, 0, sq->n);
p7_gmx_GrowTo(gx, gm->M, sq->n);
p7_MSVFilter (sq->dsq, sq->n, om, ox, &msvraw);
p7_bg_NullOne (bg, sq->dsq, sq->n, &nullsc);
msvscore = (msvraw - nullsc) / eslCONST_LOG2;
P = esl_gumbel_surv(msvscore, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
p7_GMSV(sq->dsq, sq->n, gm, gx, 2.0, &graw);
gscore = (graw - nullsc) / eslCONST_LOG2;
gP = esl_gumbel_surv(gscore, gm->evparam[p7_MMU], gm->evparam[p7_MLAMBDA]);
if (esl_opt_GetBoolean(go, "-1"))
{
printf("%-30s %-20s %9.2g %7.2f %9.2g %7.2f\n", sq->name, hmm->name, P, msvscore, gP, gscore);
}
else if (esl_opt_GetBoolean(go, "-P"))
{ /* output suitable for direct use in profmark benchmark postprocessors: */
printf("%g %.2f %s %s\n", P, msvscore, sq->name, hmm->name);
}
else
{
printf("target sequence: %s\n", sq->name);
printf("msv filter raw score: %.2f nats\n", msvraw);
printf("null score: %.2f nats\n", nullsc);
printf("per-seq score: %.2f bits\n", msvscore);
printf("P-value: %g\n", P);
printf("GMSV raw score: %.2f nats\n", graw);
printf("GSMV per-seq score: %.2f bits\n", gscore);
printf("GSMV P-value: %g\n", gP);
}
esl_sq_Reuse(sq);
}
/* cleanup */
esl_sq_Destroy(sq);
esl_sqfile_Close(sqfp);
p7_omx_Destroy(ox);
p7_gmx_Destroy(gx);
p7_oprofile_Destroy(om);
p7_profile_Destroy(gm);
p7_bg_Destroy(bg);
p7_hmm_Destroy(hmm);
p7_hmmfile_Close(hfp);
esl_alphabet_Destroy(abc);
esl_getopts_Destroy(go);
return 0;
}
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;
}
int
main(int argc, char **argv)
{
ESL_GETOPTS *go;
char *msafile;
ESL_MSAFILE *afp;
ESL_MSA *msa;
float *sqd;
int status;
int nbad;
int nali = 0;
int nbadali = 0;
int nwgt = 0;
int nbadwgt = 0;
int i;
int be_quiet;
int do_gsc;
int do_pb;
int do_blosum;
double maxid;
double tol;
int maxN;
/* Process command line
*/
go = esl_getopts_Create(options);
if (esl_opt_ProcessCmdline(go, argc, argv) != eslOK) esl_fatal("failed to parse cmd line: %s\n", go->errbuf);
if (esl_opt_VerifyConfig(go) != eslOK) esl_fatal("failed to parse cmd line: %s\n", go->errbuf);
if (esl_opt_GetBoolean(go, "-h") == TRUE) {
puts(usage);
puts("\n where options are:");
esl_opt_DisplayHelp(stdout, go, 0, 2, 80); /* 0=all docgroups; 2=indentation; 80=width */
return 0;
}
be_quiet = esl_opt_GetBoolean(go, "-q");
do_blosum = esl_opt_GetBoolean(go, "--blosum");
do_gsc = esl_opt_GetBoolean(go, "--gsc");
do_pb = esl_opt_GetBoolean(go, "--pb");
maxid = esl_opt_GetReal (go, "--id");
tol = esl_opt_GetReal (go, "--tol");
maxN = esl_opt_GetInteger(go, "--maxN");
if (esl_opt_ArgNumber(go) != 1) {
puts("Incorrect number of command line arguments.");
puts(usage);
return 1;
}
msafile = esl_opt_GetArg(go, 1);
esl_getopts_Destroy(go);
/* Weight one or more alignments from input file
*/
esl_msafile_Open(msafile, eslMSAFILE_UNKNOWN, NULL, &afp);
while (esl_msa_Read(afp, &msa) == eslOK)
{
if (maxN > 0 && msa->nseq > maxN) { esl_msa_Destroy(msa); continue; }
nali++;
nwgt += msa->nseq;
ESL_ALLOC(sqd, sizeof(float) * msa->nseq);
if (do_gsc) {
esl_msaweight_GSC(msa);
GSCWeights(msa->aseq, msa->nseq, msa->alen, sqd);
} else if (do_pb) {
esl_msaweight_PB(msa);
PositionBasedWeights(msa->aseq, msa->nseq, msa->alen, sqd);
} else if (do_blosum) {
esl_msaweight_BLOSUM(msa, maxid);
BlosumWeights(msa->aseq, msa->nseq, msa->alen, maxid, sqd);
/* workaround SQUID bug: BLOSUM weights weren't renormalized to sum to nseq. */
esl_vec_FNorm (sqd, msa->nseq);
esl_vec_FScale(sqd, msa->nseq, (float) msa->nseq);
}
if (! be_quiet) {
for (i = 0; i < msa->nseq; i++)
fprintf(stdout, "%-20s %.3f %.3f\n",
msa->sqname[i], msa->wgt[i], sqd[i]);
}
nbad = 0;
for (i = 0; i < msa->nseq; i++)
if (esl_DCompare((double) sqd[i], msa->wgt[i], tol) != eslOK)
nbad++;
if (nbad > 0) nbadali++;
nbadwgt += nbad;
if (nbad > 0) printf("%-20s :: alignment shows %d weights that differ (out of %d) \n",
msa->name, nbad, msa->nseq);
esl_msa_Destroy(msa);
free(sqd);
}
esl_msafile_Close(afp);
if (nbadali == 0)
printf("OK: all weights identical between squid and Easel in %d alignment(s)\n", nali);
else {
printf("%d of %d weights mismatched at (> %f fractional difference)\n",
nbadwgt, nwgt, tol);
printf("involving %d of %d total alignments\n", nbadali, nali);
}
return eslOK;
ERROR:
return status;
}
