CRef<objects::CPssmWithParameters>
PsiBlastComputePssmFromAlignment(const objects::CBioseq& query,
CConstRef<objects::CSeq_align_set> alignment,
CRef<objects::CScope> database_scope,
const CPSIBlastOptionsHandle& opts_handle,
CConstRef<CBlastAncillaryData> ancillary_data,
PSIDiagnosticsRequest* diagnostics_request)
{
// Extract PSSM engine options from options handle
CPSIBlastOptions opts;
PSIBlastOptionsNew(&opts);
opts->pseudo_count = opts_handle.GetPseudoCount();
opts->inclusion_ethresh = opts_handle.GetInclusionThreshold();
string query_descr = NcbiEmptyString;
if (query.IsSetDescr()) {
const CBioseq::TDescr::Tdata& data = query.GetDescr().Get();
ITERATE(CBioseq::TDescr::Tdata, iter, data) {
if((*iter)->IsTitle()) {
query_descr += (*iter)->GetTitle();
}
}
}
CBlastQuerySourceBioseqSet query_source(query, true);
string warnings;
const SBlastSequence query_seq =
query_source.GetBlastSequence(0, eBlastEncodingProtein,
eNa_strand_unknown,
eSentinels, &warnings);
_ASSERT(warnings.empty());
CPsiBlastInputData input(query_seq.data.get()+1, // skip sentinel
query_seq.length-2, // don't count sentinels
alignment, database_scope,
*opts.Get(),
opts_handle.GetMatrixName(),
opts_handle.GetGapOpeningCost(),
opts_handle.GetGapExtensionCost(),
diagnostics_request,
query_descr);
CPssmEngine engine(&input);
engine.SetUngappedStatisticalParams(ancillary_data);
CRef<CPssmWithParameters> retval(engine.Run());
PsiBlastAddAncillaryPssmData(*retval,
opts_handle.GetGapOpeningCost(),
opts_handle.GetGapExtensionCost());
return retval;
}
Int2 BLAST_InitDefaultOptions(EBlastProgramType program_number,
LookupTableOptions** lookup_options,
QuerySetUpOptions** query_setup_options,
BlastInitialWordOptions** word_options,
BlastExtensionOptions** ext_options,
BlastHitSavingOptions** hit_options,
BlastScoringOptions** score_options,
BlastEffectiveLengthsOptions** eff_len_options,
PSIBlastOptions** psi_options,
BlastDatabaseOptions** db_options)
{
Int2 status;
if ((status = LookupTableOptionsNew(program_number, lookup_options)))
return status;
if ((status=BlastQuerySetUpOptionsNew(query_setup_options)))
return status;
if ((status=BlastInitialWordOptionsNew(program_number, word_options)))
return status;
if ((status=BlastScoringOptionsNew(program_number, score_options)))
return status;
if ((status = BlastExtensionOptionsNew(program_number, ext_options,
(*score_options)->gapped_calculation)))
return status;
if ((status=BlastHitSavingOptionsNew(program_number, hit_options,
(*score_options)->gapped_calculation)))
return status;
if ((status=BlastEffectiveLengthsOptionsNew(eff_len_options)))
return status;
if ((status=PSIBlastOptionsNew(psi_options)))
return status;
if ((status=BlastDatabaseOptionsNew(db_options)))
return status;
return 0;
}
SU_PSSMInput::SU_PSSMInput(const BlockMultipleAlignment *b) : bma(b)
{
// TRACE_MESSAGE("Creating SU_PSSMInput structure");
// encode master
masterLength = bma->GetMaster()->Length();
masterNCBIStdaa = new unsigned char[masterLength];
for (unsigned int i=0; i<masterLength; ++i)
masterNCBIStdaa[i] = LookupNCBIStdaaNumberFromCharacter(bma->GetMaster()->m_sequenceString[i]);
// create PSIMsa
PSIMsaDimensions dim;
dim.query_length = bma->GetMaster()->Length();
dim.num_seqs = bma->NRows() - 1; // not including master
data = PSIMsaNew(&dim);
FillInAlignmentData(bma, data);
// set up PSIDiagnosticsRequest
diag.information_content = false;
diag.residue_frequencies = false;
diag.weighted_residue_frequencies = false;
diag.frequency_ratios = true; // true to match cdtree
diag.gapless_column_weights = false;
// create PSIBlastOptions
PSIBlastOptionsNew(&options);
options->nsg_compatibility_mode = false; // false for now, since we're not using a consensus
double infoContent = CalculateInformationContent(data, false);
if (infoContent > 84 ) options->pseudo_count = 10;
else if (infoContent > 55 ) options->pseudo_count = 7;
else if (infoContent > 43 ) options->pseudo_count = 5;
else if (infoContent > 41.5) options->pseudo_count = 4;
else if (infoContent > 40 ) options->pseudo_count = 3;
else if (infoContent > 39 ) options->pseudo_count = 2;
else options->pseudo_count = 1;
#ifdef DEBUG_PSSM
CNcbiOfstream ofs("psimsa.txt", IOS_BASE::out | IOS_BASE::app);
if (ofs) {
// diag.residue_frequencies = true;
ofs << "information content: " << setprecision(6) << infoContent << '\n'
<< "pseudocount: " << options->pseudo_count << '\n'
<< "query length: " << GetQueryLength() << '\n'
<< "query: ";
for (unsigned int i=0; i<GetQueryLength(); ++i)
ofs << LookupCharacterFromNCBIStdaaNumber(GetQuery()[i]);
ofs << "\nmatrix name: " << GetMatrixName() << '\n'
<< "options->pseudo_count: " << options->pseudo_count << '\n'
<< "options->inclusion_ethresh: " << options->inclusion_ethresh << '\n'
<< "options->use_best_alignment: " << (int) options->use_best_alignment << '\n'
<< "options->nsg_compatibility_mode: " << (int) options->nsg_compatibility_mode << '\n'
<< "options->impala_scaling_factor: " << options->impala_scaling_factor << '\n'
<< "diag->information_content: " << (int) GetDiagnosticsRequest()->information_content << '\n'
<< "diag->residue_frequencies: " << (int) GetDiagnosticsRequest()->residue_frequencies << '\n'
<< "diag->weighted_residue_frequencies: " << (int) GetDiagnosticsRequest()->weighted_residue_frequencies << '\n'
<< "diag->frequency_ratios: " << (int) GetDiagnosticsRequest()->frequency_ratios << '\n'
<< "diag->gapless_column_weights: " << (int) GetDiagnosticsRequest()->gapless_column_weights << '\n'
<< "num_seqs: " << data->dimensions->num_seqs << ", query_length: " << data->dimensions->query_length << '\n';
for (unsigned int row=0; row<=data->dimensions->num_seqs; ++row) {
for (unsigned int column=0; column<data->dimensions->query_length; ++column)
ofs << LookupCharacterFromNCBIStdaaNumber(data->data[row][column].letter);
ofs << '\n';
}
for (unsigned int row=0; row<=data->dimensions->num_seqs; ++row) {
for (unsigned int column=0; column<data->dimensions->query_length; ++column)
ofs << (data->data[row][column].is_aligned ? 'A' : 'U');
ofs << '\n';
}
}
#endif
}
