int main(int argc, char **argv) { const char *hmmfile; /* file to read HMMs from */ FILE *fp; /* output file handle */ HMMFILE *hmmfp; /* opened hmmfile for reading */ struct plan7_s *hmm; /* HMM to generate from */ int L; /* length of a sequence */ int i; /* counter over sequences */ char *ofile; /* output sequence file */ int nseq; /* number of seqs to sample */ int seed; /* random number generator seed */ int be_quiet; /* TRUE to silence header/footer */ int do_alignment; /* TRUE to output in aligned format */ int do_consensus; /* TRUE to do a single consensus seq */ AjBool ajselex; AjBool ajcons; AjPFile inf=NULL; AjPFile outf=NULL; AjPStr instr=NULL; AjPStr outstr=NULL; #ifdef MEMDEBUG unsigned long histid1, histid2, orig_size, current_size; orig_size = malloc_inuse(&histid1); fprintf(stderr, "[... memory debugging is ON ...]\n"); #endif /*********************************************** * Parse command line ***********************************************/ nseq = 10; be_quiet = FALSE; do_alignment = FALSE; do_consensus = FALSE; ofile = NULL; embInitPV("ohmmemit",argc,argv,"HMMER",VERSION); ajselex = ajAcdGetBoolean("selex"); ajcons = ajAcdGetBoolean("consensus"); nseq = ajAcdGetInt("number"); seed = ajAcdGetInt("seed"); inf = ajAcdGetInfile("infile"); outf = ajAcdGetOutfile("outfile"); if(!seed) seed = time ((time_t *) NULL); if(ajselex) do_alignment=TRUE; else do_alignment=FALSE; if(ajcons) do_consensus=TRUE; else do_consensus=FALSE; instr = ajStrNewC((char *)ajFileGetNameC(inf)); outstr = ajStrNewC((char *)ajFileGetNameC(outf)); hmmfile = ajStrGetPtr(instr); sre_srandom(seed); if (do_alignment && do_consensus) ajFatal("Sorry, -selex and -consensus are incompatible.\n"); if (nseq != 10 && do_consensus) ajWarn("-consensus overrides -number (# of sampled seqs)"); /*********************************************** * Open HMM file (might be in HMMERDB or current directory). * Read a single HMM from it. ***********************************************/ if ((hmmfp = HMMFileOpen(hmmfile, "HMMERDB")) == NULL) ajFatal("Failed to open HMM file %s\n", hmmfile); if (!HMMFileRead(hmmfp, &hmm)) ajFatal("Failed to read any HMMs from %s\n", hmmfile); HMMFileClose(hmmfp); if (hmm == NULL) ajFatal("HMM file %s corrupt or in incorrect format? Parse failed", hmmfile); /* Configure the HMM to shut off N,J,C emission: so we * do a simple single pass through the model. */ Plan7NakedConfig(hmm); Plan7Renormalize(hmm); /*********************************************** * Open the output file, or stdout ***********************************************/ fp = ajFileGetFileptr(outf); /*********************************************** * Show the options banner ***********************************************/ be_quiet=TRUE; if (! be_quiet) { printf("HMM file: %s\n", hmmfile); if (! do_consensus) { printf("Number of seqs: %d\n", nseq); printf("Random seed: %d\n", seed); } printf("- - - - - - - - - - - - - - - - - - - - - - - - - " "- - - - - - -\n\n"); } /*********************************************** * Do the work. * If we're generating an alignment, we have to collect * all our traces, then output. If we're generating unaligned * sequences, we can emit one at a time. ***********************************************/ if (do_consensus) { char *seq; SQINFO sqinfo; /* info about sequence (name/desc) */ EmitConsensusSequence(hmm, &seq, NULL, &L, NULL); strcpy(sqinfo.name, "consensus"); sqinfo.len = L; sqinfo.flags = SQINFO_NAME | SQINFO_LEN; WriteSeq(fp, kPearson, seq, &sqinfo); free(seq); } else if (do_alignment) { struct p7trace_s **tr; char **dsq; SQINFO *sqinfo; char **aseq; AINFO ainfo; float *wgt; dsq = MallocOrDie(sizeof(char *) * nseq); tr = MallocOrDie(sizeof(struct p7trace_s *) * nseq); sqinfo = MallocOrDie(sizeof(SQINFO) * nseq); wgt = MallocOrDie(sizeof(float) * nseq); FSet(wgt, nseq, 1.0); for (i = 0; i < nseq; i++) { EmitSequence(hmm, &(dsq[i]), &L, &(tr[i])); sprintf(sqinfo[i].name, "seq%d", i+1); sqinfo[i].len = L; sqinfo[i].flags = SQINFO_NAME | SQINFO_LEN; } P7Traces2Alignment(dsq, sqinfo, wgt, nseq, hmm->M, tr, FALSE, &aseq, &ainfo); /* Output the alignment */ WriteSELEX(fp, aseq, &ainfo, 50); if (ofile != NULL && !be_quiet) printf("Alignment saved in file %s\n", ofile); /* Free memory */ for (i = 0; i < nseq; i++) { P7FreeTrace(tr[i]); free(dsq[i]); } FreeAlignment(aseq, &ainfo); free(sqinfo); free(dsq); free(wgt); free(tr); } else /* unaligned sequence output */ { struct p7trace_s *tr; char *dsq; char *seq; SQINFO sqinfo; for (i = 0; i < nseq; i++) { EmitSequence(hmm, &dsq, &L, &tr); sprintf(sqinfo.name, "seq%d", i+1); sqinfo.len = L; sqinfo.flags = SQINFO_NAME | SQINFO_LEN; seq = DedigitizeSequence(dsq, L); WriteSeq(fp, kPearson, seq, &sqinfo); P7FreeTrace(tr); free(dsq); free(seq); } } ajFileClose(&outf); FreePlan7(hmm); SqdClean(); #ifdef MEMDEBUG current_size = malloc_inuse(&histid2); if (current_size != orig_size) malloc_list(2, histid1, histid2); else fprintf(stderr, "[No memory leaks.]\n"); #endif ajStrDel(&instr); ajStrDel(&outstr); ajFileClose(&inf); ajFileClose(&outf); embExit(); return 0; }
int main(int argc, char **argv) { const char *hmmfile; /* file to read HMMs from */ HMMFILE *hmmfp; /* opened hmmfile for reading */ const char *seqfile; /* file to read target sequence from */ char **rseq; /* raw, unaligned sequences */ SQINFO *sqinfo; /* info associated with sequences */ char **dsq; /* digitized raw sequences */ int nseq; /* number of sequences */ char **aseq; /* aligned sequences */ AINFO ainfo; /* alignment information */ float *wgt; /* per-sequence weights */ int i; struct plan7_s *hmm; /* HMM to align to */ struct p7trace_s **tr; /* traces for aligned sequences */ int be_quiet; /* TRUE to suppress verbose banner */ int matchonly; /* TRUE to show only match state syms */ const char *outfile; /* optional alignment output file */ FILE *ofp; /* handle on alignment output file */ AjPFile ajwithali; /* name of additional alignment file to align */ AjPFile ajmapali; /* name of additional alignment file to map */ AjBool ajmatch=ajFalse; AjPFile outf=NULL; AjPStr outfname=NULL; AjPFile inf=NULL; AjPStr infname=NULL; AjPSeqset seqset=NULL; AjPStr ajseqfile=NULL; char* mapali=NULL; char* withali=NULL; #ifdef MEMDEBUG unsigned long histid1, histid2, orig_size, current_size; orig_size = malloc_inuse(&histid1); fprintf(stderr, "[... memory debugging is ON ...]\n"); #endif /*********************************************** * Parse command line ***********************************************/ matchonly = FALSE; outfile = NULL; be_quiet = FALSE; withali = NULL; mapali = NULL; embInitPV("ohmmalign",argc,argv,"HMMER",VERSION); ajmatch = ajAcdGetBoolean("matchonly"); if(ajmatch) matchonly=TRUE; else matchonly=FALSE; ajmapali = ajAcdGetInfile("mapalifile"); if (ajmapali) mapali = ajCharNewS(ajFileGetNameS(ajmapali)); ajFileClose(&ajmapali); ajwithali = ajAcdGetInfile("withalifile"); if (ajwithali) withali = ajCharNewS(ajFileGetNameS(ajwithali)); ajFileClose(&ajwithali); be_quiet=TRUE; outf = ajAcdGetOutfile("outfile"); outfname = ajStrNewC((char *)ajFileGetNameC(outf)); if(*ajStrGetPtr(outfname)>31) ajFileClose(&outf); outfile = ajStrGetPtr(outfname); inf = ajAcdGetInfile("hmmfile"); infname = ajStrNewC((char *)ajFileGetNameC(inf)); ajFileClose(&inf); hmmfile = ajStrGetPtr(infname); seqset = ajAcdGetSeqset("sequences"); ajseqfile = ajStrNewC(ajStrGetPtr(seqset->Filename)); seqfile = ajStrGetPtr(ajseqfile); /*********************************************** * Open HMM file (might be in HMMERDB or current directory). * Read a single HMM from it. * * Currently hmmalign disallows the J state and * only allows one domain per sequence. To preserve * the S/W entry information, the J state is explicitly * disallowed, rather than calling a Plan7*Config() function. * this is a workaround in 2.1 for the 2.0.x "yo!" bug. ***********************************************/ if ((hmmfp = HMMFileOpen(hmmfile, "HMMERDB")) == NULL) ajFatal("Failed to open HMM file %s\n", hmmfile); if (!HMMFileRead(hmmfp, &hmm)) ajFatal("Failed to read any HMMs from %s\n", hmmfile); HMMFileClose(hmmfp); if (hmm == NULL) ajFatal("HMM file %s corrupt or in incorrect format? Parse failed", hmmfile); hmm->xt[XTE][MOVE] = 1.; /* only 1 domain/sequence ("global" alignment) */ hmm->xt[XTE][LOOP] = 0.; P7Logoddsify(hmm, TRUE); /* do we have the map we might need? */ if (mapali != NULL && ! (hmm->flags & PLAN7_MAP)) ajFatal("HMMER: HMM file %s has no map; you can't use --mapali.", hmmfile); /*********************************************** * Open sequence file in current directory. * Read all seqs from it. ***********************************************/ /* if (! SeqfileFormat(seqfile, &format, NULL)) switch (squid_errno) { case SQERR_NOFILE: ajFatal("Sequence file %s could not be opened for reading", seqfile); case SQERR_FORMAT: default: ajFatal("Failed to determine format of sequence file %s", seqfile); } if (! ReadMultipleRseqs(seqfile, format, &rseq, &sqinfo, &nseq)) ajFatal("Failed to read any sequences from file %s", seqfile); */ emboss_rseqs(seqset,&rseq,&sqinfo,&nseq); /*********************************************** * Show the banner ***********************************************/ be_quiet=TRUE; if (! be_quiet) { /* Banner(stdout, banner); */ printf( "HMM file: %s\n", hmmfile); printf( "Sequence file: %s\n", seqfile); printf("- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n"); } /*********************************************** * Do the work ***********************************************/ /* Allocations and initializations. */ dsq = MallocOrDie(sizeof(char *) * nseq); tr = MallocOrDie(sizeof(struct p7trace_s *) * nseq); /* Align each sequence to the model, collect traces */ for (i = 0; i < nseq; i++) { dsq[i] = DigitizeSequence(rseq[i], sqinfo[i].len); if (P7ViterbiSize(sqinfo[i].len, hmm->M) <= RAMLIMIT) (void) P7Viterbi(dsq[i], sqinfo[i].len, hmm, &(tr[i])); else (void) P7SmallViterbi(dsq[i], sqinfo[i].len, hmm, &(tr[i])); } /* Include an aligned alignment, if desired. */ if (mapali != NULL) include_alignment(mapali, hmm, TRUE, &rseq, &dsq, &sqinfo, &tr, &nseq); if (withali != NULL) include_alignment(withali, hmm, FALSE, &rseq, &dsq, &sqinfo, &tr, &nseq); /* Turn traces into a multiple alignment */ wgt = MallocOrDie(sizeof(float) * nseq); FSet(wgt, nseq, 1.0); P7Traces2Alignment(dsq, sqinfo, wgt, nseq, hmm->M, tr, matchonly, &aseq, &ainfo); /*********************************************** * Output the alignment ***********************************************/ if (outfile != NULL && (ofp = fopen(outfile, "w")) != NULL) { WriteSELEX(ofp, aseq, &ainfo, 50); printf("Alignment saved in file %s\n", outfile); fclose(ofp); } else WriteSELEX(stdout, aseq, &ainfo, 50); /*********************************************** * Cleanup and exit ***********************************************/ for (i = 0; i < nseq; i++) { P7FreeTrace(tr[i]); FreeSequence(rseq[i], &(sqinfo[i])); free(dsq[i]); } FreeAlignment(aseq, &ainfo); FreePlan7(hmm); free(sqinfo); free(rseq); free(dsq); free(wgt); free(tr); SqdClean(); ajStrDel(&outfname); ajStrDel(&infname); ajStrDel(&ajseqfile); #ifdef MEMDEBUG current_size = malloc_inuse(&histid2); if (current_size != orig_size) malloc_list(2, histid1, histid2); else fprintf(stderr, "[No memory leaks.]\n"); #endif ajSeqsetDel(&seqset); ajFileClose(&ajwithali); ajFileClose(&ajmapali); embExit(); return 0; }