/////////////////////////////////////////////////////////////////////////////////////
// Do precalculations for q and t to prepare comparison
/////////////////////////////////////////////////////////////////////////////////////
void PrepareTemplate(HMM& q, HMM& t, int format)
{
if (format==0) // HHM format
{
// Add transition pseudocounts to template
t.AddTransitionPseudocounts();
// Don't use CS-pseudocounts because of runtime!!!
// Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
t.PreparePseudocounts();
// Add amino acid pseudocounts to query: p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
t.AddAminoAcidPseudocounts(par.pcm, par.pca, par.pcb, par.pcc);
t.CalculateAminoAcidBackground();
}
else // HHMER format
{
// Don't add transition pseudocounts to template
// t.AddTransitionPseudocounts(par.gapd, par.gape, par.gapf, par.gapg, par.gaph, par.gapi, 0.0);
// Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
// t.PreparePseudocounts();
// DON'T ADD amino acid pseudocounts to temlate: pcm=0! t.p[i][a] = t.f[i][a]
t.AddAminoAcidPseudocounts(0, par.pca, par.pcb, par.pcc);
t.CalculateAminoAcidBackground();
}
if (par.forward>=1) t.Log2LinTransitionProbs(1.0);
// Factor Null model into HMM t
// ATTENTION! t.p[i][a] is divided by pnul[a] (for reasons of efficiency) => do not reuse t.p
t.IncludeNullModelInHMM(q,t); // Can go BEFORE the loop if not dependent on template
return;
}
// Read input file (HMM, HHM, or alignment format), and add pseudocounts etc.
void ReadAndPrepare(char* infile, HMM& q, Alignment* qali=NULL)
{
char path[NAMELEN];
// Open query file and determine file type
char line[LINELEN]=""; // input line
FILE* inf=NULL;
if (strcmp(infile,"stdin"))
{
inf = fopen(infile, "r");
if (!inf) OpenFileError(infile);
Pathname(path,infile);
}
else
{
inf = stdin;
if (v>=2) printf("Reading HMM / multiple alignment from standard input ...\n(To get a help list instead, quit and type %s -h.)\n",program_name);
*path='\0';
}
fgetline(line,LINELEN-1,inf);
// Is it an hhm file?
if (!strncmp(line,"NAME",4) || !strncmp(line,"HH",2))
{
if (v>=2) cout<<"Query file is in HHM format\n";
// Rewind to beginning of line and read query hhm file
rewind(inf);
q.Read(inf,path);
if (v>=2 && q.Neff_HMM>11.0)
fprintf(stderr,"WARNING: HMM %s looks too diverse (Neff=%.1f>11). Better check the underlying alignment... \n",q.name,q.Neff_HMM);
// Add transition pseudocounts to query -> q.p[i][a]
q.AddTransitionPseudocounts();
if (!*par.clusterfile) { //compute context-specific pseudocounts?
// Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
q.PreparePseudocounts();
// Add amino acid pseudocounts to query: q.p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
q.AddAminoAcidPseudocounts(par.pcm, par.pca, par.pcb, par.pcc);;
} else {
// Add context specific pseudocount to query
q.AddContextSpecificPseudocounts(par.pcm);
}
q.CalculateAminoAcidBackground();
}
// ... or is it an a2m/a3m alignment file
else if (line[0]=='#' || line[0]=='>')
{
Alignment* pali;
if (qali==NULL) pali=new(Alignment); else pali=qali;
if (par.calibrate) {
printf("\nError in %s: only HHM files can be calibrated.\n",program_name);
printf("Build an HHM file from your alignment with 'hhmake -i %s' and rerun hhsearch with the hhm file\n\n",infile);
exit(1);
}
if (v>=2 && strcmp(infile,"stdin")) cout<<infile<<" is in A2M, A3M or FASTA format\n";
// Read alignment from infile into matrix X[k][l] as ASCII (and supply first line as extra argument)
pali->Read(inf,infile,line);
// Convert ASCII to int (0-20),throw out all insert states, record their number in I[k][i]
// and store marked sequences in name[k] and seq[k]
pali->Compress(infile);
// Sort out the nseqdis most dissimilar sequences for display in the output alignments
pali->FilterForDisplay(par.max_seqid,par.coverage,par.qid,par.qsc,par.nseqdis);
// Remove sequences with seq. identity larger than seqid percent (remove the shorter of two)
pali->N_filtered = pali->Filter(par.max_seqid,par.coverage,par.qid,par.qsc,par.Ndiff);
if (par.Neff>=0.999)
pali->FilterNeff();
// Calculate pos-specific weights, AA frequencies and transitions -> f[i][a], tr[i][a]
pali->FrequenciesAndTransitions(q);
if (v>=2 && q.Neff_HMM>11.0)
fprintf(stderr,"WARNING: alignment %s looks too diverse (Neff=%.1f>11). Better check it with an alignment viewer... \n",q.name,q.Neff_HMM);
// Add transition pseudocounts to query -> p[i][a]
q.AddTransitionPseudocounts();
if (!*par.clusterfile) { //compute context-specific pseudocounts?
// Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
q.PreparePseudocounts();
// Add amino acid pseudocounts to query: p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
q.AddAminoAcidPseudocounts(par.pcm, par.pca, par.pcb, par.pcc);
} else {
// Add context specific pseudocount to query
q.AddContextSpecificPseudocounts(par.pcm);
}
q.CalculateAminoAcidBackground();
if (qali==NULL) delete(pali);
} else if (!strncmp(line,"HMMER",5)) {
///////////////////////////////////////////////////////////////////////////////////////
// Don't allow HMMER format as input due to the severe loss of sensitivity!!!! (only allowed in HHmake)
if (strncmp(program_name,"hhmake",6)) {
cerr<<endl<<"Error in "<<program_name<<": HMMER format not allowed as input due to the severe loss of sensitivity!\n";
exit(1);
}
// Is infile a HMMER3 file?
if (!strncmp(line,"HMMER3",6))
{
if (v>=2) cout<<"Query file is in HMMER3 format\n";
// Read 'query HMMER file
rewind(inf);
q.ReadHMMer3(inf,path);
// Don't add transition pseudocounts to query!!
// DON'T ADD amino acid pseudocounts to query: pcm=0! q.p[i][a] = f[i][a]
q.AddAminoAcidPseudocounts(0, par.pca, par.pcb, par.pcc);
q.CalculateAminoAcidBackground();
}
// ... or is infile an old HMMER file?
else if (!strncmp(line,"HMMER",5))
{
if (v>=2) cout<<"Query file is in HMMER format\n";
// Read 'query HMMER file
rewind(inf);
q.ReadHMMer(inf,path);
// DON'T ADD amino acid pseudocounts to query: pcm=0! q.p[i][a] = f[i][a]
q.AddAminoAcidPseudocounts(0, par.pca, par.pcb, par.pcc);
q.CalculateAminoAcidBackground();
}
} else {
cerr<<endl<<"Error in "<<program_name<<": unrecognized input file format in \'"<<infile<<"\'\n";
cerr<<"line = "<<line<<"\n";
exit(1);
}
fclose(inf);
if (par.addss==1)
CalculateSS(q);
if (par.columnscore == 5 && !q.divided_by_local_bg_freqs) q.DivideBySqrtOfLocalBackgroundFreqs(par.half_window_size_local_aa_bg_freqs);
if (par.forward>=1) q.Log2LinTransitionProbs(1.0);
return;
}
/////////////////////////////////////////////////////////////////////////////////////
//// MAIN PROGRAM
/////////////////////////////////////////////////////////////////////////////////////
int main(int argc, char **argv) {
char* argv_conf[MAXOPT]; // Input arguments from .hhdefaults file (first=1: argv_conf[0] is not used)
int argc_conf; // Number of arguments in argv_conf
strcpy(par.infile, "");
strcpy(par.outfile, "");
strcpy(par.alnfile, "");
//Default parameter settings
par.nseqdis = MAXSEQ - 1; // maximum number of sequences to be written
par.showcons = 0;
par.cons = 1;
par.Ndiff = 0;
par.max_seqid = 100;
par.coverage = 0;
par.pc_hhm_context_engine.pca = 0.0; // no amino acid pseudocounts
par.pc_hhm_nocontext_a = 0.0; // no amino acid pseudocounts
par.gapb = 0.0; // no transition pseudocounts
// Make command line input globally available
par.argv = argv;
par.argc = argc;
RemovePathAndExtension(program_name, argv[0]);
// Enable changing verbose mode before defaults file and command line are processed
int v = 2;
for (int i = 1; i < argc; i++) {
if (!strcmp(argv[i], "-def"))
par.readdefaultsfile = 1;
else if (strcmp(argv[i], "-v") == 0) {
v = atoi(argv[i + 1]);
}
}
par.v = Log::from_int(v);
Log::reporting_level() = par.v;
par.SetDefaultPaths();
// Read .hhdefaults file?
if (par.readdefaultsfile) {
// Process default otpions from .hhconfig file
ReadDefaultsFile(argc_conf, argv_conf);
ProcessArguments(argc_conf, argv_conf);
}
// Process command line options (they override defaults from .hhdefaults file)
ProcessArguments(argc, argv);
Alignment* qali = new Alignment(MAXSEQ, par.maxres);
HMM* q = new HMM(MAXSEQDIS, par.maxres); //Create a HMM with maximum of par.maxres match states
// q is only available after maxres is known, so we had to move this here
for (int i = 1; i <= argc - 1; i++) {
if (!strcmp(argv[i], "-name") && (i < argc - 1)) {
strmcpy(q->name, argv[++i], NAMELEN - 1); //copy longname to name...
strmcpy(q->longname, argv[i], DESCLEN - 1); //copy full name to longname
}
}
// Check command line input and default values
if (!*par.infile) {
help();
HH_LOG(ERROR) << "Input file is missing!" << std::endl;
exit(4);
}
// Get basename
RemoveExtension(q->file, par.infile); //Get basename of infile (w/o extension):
// Outfile not given? Name it basename.hhm
if (!*par.outfile && !*par.alnfile) {
RemoveExtension(par.outfile, par.infile);
strcat(par.outfile, ".seq");
}
// Prepare CS pseudocounts lib
if (!par.nocontxt && *par.clusterfile) {
InitializePseudocountsEngine(par, context_lib, crf, pc_hhm_context_engine,
pc_hhm_context_mode, pc_prefilter_context_engine,
pc_prefilter_context_mode);
}
// Set substitution matrix; adjust to query aa distribution if par.pcm==3
SetSubstitutionMatrix(par.matrix, pb, P, R, S, Sim);
// Read input file (HMM, HHM, or alignment format), and add pseudocounts etc.
char input_format = 0;
ReadQueryFile(par, par.infile, input_format, par.wg, q, qali, pb, S, Sim);
// Same code as in PrepareQueryHMM(par.infile,input_format,q,qali), except that we add SS prediction
// Add Pseudocounts, if no HMMER input
if (input_format == 0) {
// Transform transition freqs to lin space if not already done
q->AddTransitionPseudocounts(par.gapd, par.gape, par.gapf, par.gapg,
par.gaph, par.gapi, par.gapb, par.gapb);
// Comput substitution matrix pseudocounts
if (par.nocontxt) {
// Generate an amino acid frequency matrix from f[i][a] with full pseudocount admixture (tau=1) -> g[i][a]
q->PreparePseudocounts(R);
// Add amino acid pseudocounts to query: p[i][a] = (1-tau)*f[i][a] + tau*g[i][a]
q->AddAminoAcidPseudocounts(par.pc_hhm_nocontext_mode,
par.pc_hhm_nocontext_a, par.pc_hhm_nocontext_b,
par.pc_hhm_nocontext_c);
}
else {
// Add full context specific pseudocounts to query
q->AddContextSpecificPseudocounts(pc_hhm_context_engine,
pc_hhm_context_mode);
}
}
else {
q->AddAminoAcidPseudocounts(0, par.pc_hhm_nocontext_a,
par.pc_hhm_nocontext_b, par.pc_hhm_nocontext_c);
}
q->CalculateAminoAcidBackground(pb);
if (par.columnscore == 5 && !q->divided_by_local_bg_freqs)
q->DivideBySqrtOfLocalBackgroundFreqs(
par.half_window_size_local_aa_bg_freqs, pb);
// Write consensus sequence to sequence file
// Consensus sequence is calculated in hhalignment.C, Alignment::FrequenciesAndTransitions()
if (*par.outfile) {
FILE* outf = NULL;
if (strcmp(par.outfile, "stdout")) {
outf = fopen(par.outfile, "a");
if (!outf)
OpenFileError(par.outfile, __FILE__, __LINE__, __func__);
}
else
outf = stdout;
// OLD
//// ">name_consensus" -> ">name consensus"
//strsubst(q->sname[q->nfirst],"_consensus"," consensus");
//fprintf(outf,">%s\n%s\n",q->sname[q->nfirst],q->seq[q->nfirst]+1);
// NEW (long header needed for NR30cons database)
fprintf(outf, ">%s\n%s\n", q->longname, q->seq[q->nfirst] + 1);
fclose(outf);
}
// Print A3M/A2M/FASTA output alignment
if (*par.alnfile) {
HalfAlignment qa;
int n = imin(q->n_display,
par.nseqdis + (q->nss_dssp >= 0) + (q->nss_pred >= 0)
+ (q->nss_conf >= 0) + (q->ncons >= 0));
qa.Set(q->name, q->seq, q->sname, n, q->L, q->nss_dssp, q->nss_pred,
q->nss_conf, q->nsa_dssp, q->ncons);
if (par.outformat == 1)
qa.BuildFASTA();
else if (par.outformat == 2)
qa.BuildA2M();
else if (par.outformat == 3)
qa.BuildA3M();
if (qali->readCommentLine)
qa.Print(par.alnfile, par.append, qali->longname); // print alignment to outfile
else
qa.Print(par.alnfile, par.append); // print alignment to outfile
}
delete qali;
delete q;
DeletePseudocountsEngine(context_lib, crf, pc_hhm_context_engine,
pc_hhm_context_mode, pc_prefilter_context_engine,
pc_prefilter_context_mode);
}
