CRef<CSeq_entry> CAlnReader::GetSeqEntry()
{
if (m_Entry) {
return m_Entry;
} else if ( !m_ReadDone ) {
NCBI_THROW2(CObjReaderParseException, eFormat,
"CAlnReader::GetSeqEntry(): "
"Seq_entry is not available until after Read()", 0);
}
m_Entry = new CSeq_entry();
CRef<CSeq_annot> seq_annot (new CSeq_annot);
seq_annot->SetData().SetAlign().push_back(GetSeqAlign());
m_Entry->SetSet().SetClass(CBioseq_set::eClass_pop_set);
m_Entry->SetSet().SetAnnot().push_back(seq_annot);
CBioseq_set::TSeq_set& seq_set = m_Entry->SetSet().SetSeq_set();
typedef CDense_seg::TDim TNumrow;
for (TNumrow row_i = 0; row_i < m_Dim; row_i++) {
const string& seq_str = m_SeqVec[row_i];
const size_t& seq_str_len = seq_str.size();
CRef<CSeq_entry> seq_entry (new CSeq_entry);
// seq-id(s)
CBioseq::TId& ids = seq_entry->SetSeq().SetId();
CSeq_id::ParseFastaIds(ids, m_Ids[row_i], true);
if (ids.empty()) {
ids.push_back(CRef<CSeq_id>(new CSeq_id(CSeq_id::e_Local,
m_Ids[row_i])));
}
// mol
CSeq_inst::EMol mol = CSeq_inst::eMol_not_set;
CSeq_id::EAccessionInfo ai = ids.front()->IdentifyAccession();
if (ai & CSeq_id::fAcc_nuc) {
mol = CSeq_inst::eMol_na;
} else if (ai & CSeq_id::fAcc_prot) {
mol = CSeq_inst::eMol_aa;
} else {
switch (CFormatGuess::SequenceType(seq_str.data(), seq_str_len)) {
case CFormatGuess::eNucleotide: mol = CSeq_inst::eMol_na; break;
case CFormatGuess::eProtein: mol = CSeq_inst::eMol_aa; break;
default: break;
}
}
// seq-inst
CRef<CSeq_inst> seq_inst (new CSeq_inst);
seq_entry->SetSeq().SetInst(*seq_inst);
seq_set.push_back(seq_entry);
// repr
seq_inst->SetRepr(CSeq_inst::eRepr_raw);
// mol
seq_inst->SetMol(mol);
// len
_ASSERT(seq_str_len == m_SeqLen[row_i]);
seq_inst->SetLength(seq_str_len);
// data
CSeq_data& data = seq_inst->SetSeq_data();
if (mol == CSeq_inst::eMol_aa) {
data.SetIupacaa().Set(seq_str);
} else {
data.SetIupacna().Set(seq_str);
CSeqportUtil::Pack(&data);
}
}
return m_Entry;
}
int CLocalFinderApp::Run(void)
{
CArgs myargs = GetArgs();
int left = myargs["from"].AsInteger();
int right = myargs["to"].AsInteger();
bool repeats = myargs["rep"];
//
// read our sequence data
//
CFastaReader fastareader(myargs["input"].AsString());
CRef<CSeq_loc> masked_regions;
masked_regions = fastareader.SaveMask();
CRef<CSeq_entry> se = fastareader.ReadOneSeq();
if(masked_regions) {
CBioseq& bioseq = se->SetSeq(); // assumes that reader gets only one sequence per fasta id (no [] in file)
CRef<CSeq_annot> seq_annot(new CSeq_annot);
seq_annot->SetNameDesc("NCBI-FASTA-Lowercase");
bioseq.SetAnnot().push_back(seq_annot);
CSeq_annot::C_Data::TFtable* feature_table = &seq_annot->SetData().SetFtable();
for(CSeq_loc_CI i(*masked_regions); i; ++i) {
CRef<CSeq_feat> repeat(new CSeq_feat);
CRef<CSeq_id> id(new CSeq_id);
id->Assign(i.GetSeq_id());
CRef<CSeq_loc> loc(new CSeq_loc(*id, i.GetRange().GetFrom(), i.GetRange().GetTo()));
repeat->SetLocation(*loc);
repeat->SetData().SetImp().SetKey("repeat_region");
feature_table->push_back(repeat);
}
}
CRef<CObjectManager> objmgr = CObjectManager::GetInstance();
CScope scope(*objmgr);
scope.AddTopLevelSeqEntry(*se);
CRef<CSeq_id> cntg(new CSeq_id);
cntg->Assign(*se->GetSeq().GetFirstId());
CSeq_loc loc;
loc.SetWhole(*cntg);
CSeqVector vec(loc, scope);
vec.SetIupacCoding();
CResidueVec seq;
ITERATE(CSeqVector,i,vec)
seq.push_back(*i);
// read the alignment information
TGeneModelList alignments;
if(myargs["align"]) {
CNcbiIstream& alignmentfile = myargs["align"].AsInputFile();
string our_contig = cntg->GetSeqIdString(true);
string cur_contig;
CAlignModel algn;
while(alignmentfile >> algn >> getcontig(cur_contig)) {
if (cur_contig==our_contig)
alignments.push_back(algn);
}
}
// create engine
CRef<CHMMParameters> hmm_params(new CHMMParameters(myargs["model"].AsInputFile()));
CGnomonEngine gnomon(hmm_params, seq, TSignedSeqRange(left, right));
// run!
gnomon.Run(alignments, repeats, true, true, false, false, 10.0);
// dump the annotation
CRef<CSeq_annot> annot = gnomon.GetAnnot(*cntg);
auto_ptr<CObjectOStream> os(CObjectOStream::Open(eSerial_AsnText, cout));
*os << *annot;
return 0;
}
