int
main(int argc, char **argv)
{
char *cmfile;
ESL_ALPHABET *abc;
char *seqfile;
ESL_SQFILE *sqfp;
int format;
CM_FILE *cmfp;
CM_t *cm;
ESL_SQ *seq;
float sc, rev_sc;
Parsetree_t *tr;
Fancyali_t *fali;
Fancyali_t *rev_fali;
int do_local;
/* int status; */
/* char *optname; */
/* char *optarg; */
int optind;
int status;
char errbuf[eslERRBUFSIZE];
cmfile = seqfile = NULL;
abc = NULL;
sqfp = NULL;
cmfp = NULL;
cm = NULL;
seq = NULL;
tr = NULL;
fali = NULL;
rev_fali = NULL;
format = eslSQFILE_UNKNOWN;
do_local = TRUE;
/* Should process options, but for now assume none and set optind */
optind = 1;
if ( argc - optind != 2 ) cm_Die("Incorrect number of arguments\n");
cmfile = argv[optind++];
seqfile = argv[optind++];
if((status = cm_file_Open(cmfile, NULL, FALSE, &cmfp, errbuf)) != eslOK)
cm_Die("Failed to open covariance model save file\n");
if ((status = cm_file_Read(cmfp, TRUE, &abc, &cm)) != eslOK)
cm_Die("Failed to read a CM from cm file\n");
if (cm == NULL)
cm_Die("CM file empty?\n");
cm_file_Close(cmfp);
if ( esl_sqfile_Open(seqfile, format, NULL, &sqfp) != eslOK )
cm_Die("Failed to open sequence database file\n");
if (do_local) cm->config_opts |= CM_CONFIG_LOCAL;
if((status = cm_Configure(cm, errbuf, -1)) != eslOK) cm_Die(errbuf);
/*SetMarginalScores_reproduce_bug_i27(cm);*/
seq = esl_sq_Create();
while ( esl_sqio_Read(sqfp, seq) == eslOK )
{
if (seq->n == 0) continue;
int i0 = 1;
int j0 = seq->n;
if (seq->dsq == NULL)
esl_sq_Digitize(abc, seq);
sc = TrCYK_DnC(cm, seq->dsq, seq->n, 0, i0, j0, PLI_PASS_5P_AND_3P_ANY, TRUE, &tr); /* TRUE: reproduce v1.0 behavior */
/* sc = TrCYK_Inside(cm, seq->dsq, seq->n, 0, i0, j0, PLI_PASS_5P_AND_3P_ANY, TRUE, FALSE, &tr); */
fali = CreateFancyAli(cm->abc, tr, cm, cm->cmcons, seq->dsq, FALSE, NULL);
/* float sc, struct_sc;
* ParsetreeScore(cm, NULL, NULL, tr, seq->dsq, FALSE, &sc, &struct_sc, NULL, NULL, NULL);
* printf("Parsetree score: %.4f\n", sc);
* ParsetreeDump(stdout, tr, cm, seq->dsq);
*/
FreeParsetree(tr);
revcomp(abc, seq, seq);
rev_sc = TrCYK_DnC(cm,seq->dsq, seq->n, 0, i0, j0, PLI_PASS_5P_AND_3P_ANY, TRUE, &tr); /* TRUE: reproduce v1.0 behavior */
rev_fali = CreateFancyAli(cm->abc, tr, cm, cm->cmcons,seq->dsq, FALSE, NULL);
/*ParsetreeDump(stdout, tr, cm, seq->dsq);*/
FreeParsetree(tr);
if (sc > rev_sc)
{
printf("sequence: %s\n", seq->name);
printf("score: %.2f\n",sc);
PrintFancyAli(stdout, fali, 0, FALSE, FALSE, 60);
}
else
{
printf("sequence: %s (reversed)\n", seq->name);
printf("score: %.2f\n",rev_sc);
PrintFancyAli(stdout, fali, seq->n, TRUE, FALSE, 60);
}
FreeFancyAli(fali);
FreeFancyAli(rev_fali);
esl_sq_Destroy(seq);
seq = esl_sq_Create();
}
esl_sq_Destroy(seq);
FreeCM(cm);
esl_sqfile_Close(sqfp);
return EXIT_SUCCESS;
}
int main(int argc, char **argv)
{
ESL_SQFILE *sqfp = NULL;
ESL_SQ *sq = NULL;
ESL_SQ *dsq = NULL;
ESL_SQ **prot;
int c;
ESL_ALPHABET *abc, *prot_abc;
ESL_SQ *prot6[6];
int x;
abc = esl_alphabet_Create(eslDNA);
prot_abc = esl_alphabet_Create(eslAMINO);
if(argc != 2)
{
printf("You need to pass an argument for a filepath to a dna/rna fasta file\n");
exit(0);
}
if(eslOK != esl_sqfile_Open(argv[1], eslSQFILE_FASTA, NULL, &sqfp))
{
printf("Invalid filepath: %s\n", argv[1]);
exit(0);
}
sq = esl_sq_Create();
if(sq == NULL)
{
printf("could not allocate new sequence\n");
exit(0);
}
if(esl_sqio_Read(sqfp, sq) != eslOK)
{
printf("Not a valid fasta file %s\n", argv[1]);
exit(0);
}
dsq = esl_sq_Create();
if(dsq == NULL)
{
printf("could not allocate digital sequence\n");
exit(0);
}
if(esl_sq_Copy(sq, dsq) != eslOK)
{
printf("could not copy sequence\n");
exit(0);
}
if(esl_sq_Digitize(abc, dsq) != eslOK)
{
printf("could not digitize sequence\n");
exit(0);
}
esl_sqio_Write(stdout, sq, eslSQFILE_FASTA, 0);
if(esl_trans_6frame(sq, prot6) != eslOK)
{
printf("could not generate six frame translation\n");
exit(0);
}
for(x = 0; x < 6; x++)
{
esl_sqio_Write(stdout, prot6[x], eslSQFILE_FASTA, 0);
}
if(esl_trans_orf(dsq, &prot, &c, 10) != eslOK)
{
printf("could not translate open reading frames\n");
exit(0);
}
for(x = 0; x < c; x++)
{
esl_sqio_Write(stdout, prot[x], eslSQFILE_FASTA, 0);
}
return 0;
}
void run_hmmer_pipeline(const char* seq) {
int index, i, status;
ESL_SQ* sq = esl_sq_CreateFrom(NULL, seq, NULL, NULL, NULL);
P7_OPROFILE *om = NULL;
P7_PROFILE *gm = NULL;
float usc, vfsc, fwdsc; /* filter scores */
float filtersc; /* HMM null filter score */
float nullsc; /* null model score */
float seqbias;
float seq_score; /* the corrected per-seq bit score */
double P;
WRAPPER_RESULT* result;
num_results = 0;
if(sq->n == 0) {
esl_sq_Destroy(sq);
return;
}
esl_sq_Digitize(abc, sq);
int n = 0;
float oasc;
for(index = 0;index < num_models;index++) {
om = models[index];
p7_omx_Reuse(oxf);
p7_omx_Reuse(oxb);
p7_omx_GrowTo(oxf, om->M, sq->n, sq->n);
p7_omx_GrowTo(oxb, om->M, sq->n, sq->n);
p7_oprofile_ReconfigLength(om, sq->n);
p7_bg_SetFilter(bg, om->M, om->compo);
p7_bg_SetLength(bg, sq->n);
//Calibrate null model
p7_bg_NullOne(bg, sq->dsq, sq->n, &nullsc);
//MSV Filter
p7_MSVFilter(sq->dsq, sq->n, om, oxf, &usc);
seq_score = (usc - nullsc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
if (P > f1) continue;
//Bias filter (model compo)
p7_bg_FilterScore(bg, sq->dsq, sq->n, &filtersc);
seq_score = (usc - filtersc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_MMU], om->evparam[p7_MLAMBDA]);
if (P > f1) continue;
//Viterbi filter (Only do if P value from Bias is high)
if(P > f2) {
p7_ViterbiFilter(sq->dsq, sq->n, om, oxf, &vfsc);
seq_score = (vfsc - filtersc) / eslCONST_LOG2;
P = esl_gumbel_surv(seq_score, om->evparam[p7_VMU], om->evparam[p7_VLAMBDA]);
if (P > f2) continue;
}
//Get the real probability (forward)
p7_Forward(sq->dsq, sq->n, om, oxf, &fwdsc);
seq_score = (fwdsc - filtersc) / eslCONST_LOG2;
P = esl_exp_surv(seq_score, om->evparam[p7_FTAU], om->evparam[p7_FLAMBDA]);
if(hmmer_error) {
fprintf(stderr, "HMM: %s, seq: %s", om->name, seq);
hmmer_error = 0;
continue;
}
if (P > f3) continue;
//Real hit, go in to posterior decoding and alignment
p7_omx_Reuse(oxb);
p7_trace_Reuse(tr);
p7_Backward(sq->dsq, sq->n, om, oxf, oxb, NULL);
status = p7_Decoding(om, oxf, oxb, oxb);
if(status == eslOK) {
//And then trace the result
p7_OptimalAccuracy(om, oxb, oxf, &oasc);
p7_OATrace(om, oxb, oxf, tr);
} else if(status == eslERANGE) {
fprintf(stderr, "Decoding overflow on model %s\n", om->name);
gm = gmodels[index];
if(gxf == NULL) {
gxf = p7_gmx_Create(gm->M, sq->n);
gxb = p7_gmx_Create(gm->M, sq->n);
} else {
p7_gmx_GrowTo(gxf, gm->M, sq->n);
p7_gmx_GrowTo(gxb, gm->M, sq->n);
}
p7_ReconfigLength(gm, sq->n);
p7_GForward (sq->dsq, sq->n, gm, gxf, &fwdsc);
p7_GBackward(sq->dsq, sq->n, gm, gxb, NULL);
p7_GDecoding(gm, gxf, gxb, gxb);
p7_GOptimalAccuracy(gm, gxb, gxf, &oasc);
p7_GOATrace (gm, gxb, gxf, tr);
p7_gmx_Reuse(gxf);
p7_gmx_Reuse(gxb);
}
if(hmmer_error) {
fprintf(stderr, "HMM: %s, seq: %s", om->name, seq);
hmmer_error = 0;
continue;
}
result = wrapper_results[num_results];
reuse_result(result, tr->N + om->M, om->name); //We're way overallocating here, but it's hard to know at this point how much space we'll need for the alignment (plus leading and trailing gaps)
trace_into(tr, result, sq, abc, om->M);
result->bits = seq_score;
num_results++;
}
esl_sq_Destroy(sq);
}
