SCompartmentData(const CSeq_align_set &compartment)
: num_alignments(compartment.Get().size())
{
CSeq_align align;
align.SetSegs().SetDisc(const_cast<CSeq_align_set &>(compartment));
query_range = align.GetSeqRange(0);
subject_range = align.GetSeqRange(1);
}
int CTestCompartApplication::Run(void)
{
// Get arguments
const CArgs& args = GetArgs();
CRef<CObjectManager> om(CObjectManager::GetInstance());
CGBDataLoader::RegisterInObjectManager(*om);
CRef<CScope> scope(new CScope(*om));
scope->AddDefaults();
list< CRef<CSeq_align> > aligns;
{{
CNcbiIstream& istr = args["i"].AsInputFile();
auto_ptr<CObjectIStream> is
(CObjectIStream::Open(eSerial_AsnText, istr));
while ( !is->EndOfData() ) {
CRef<CSeq_align> align(new CSeq_align);
*is >> *align;
aligns.push_back(align);
}
}}
CNcbiOstream& ostr = args["o"].AsOutputFile();
TCompartOptions opts = fCompart_Defaults;
if (args["allow-intersect"]) {
opts |= fCompart_AllowIntersections;
}
if (args["allow-intersect-query"]) {
opts |= fCompart_AllowIntersectionsQuery;
}
if (args["allow-intersect-subject"]) {
opts |= fCompart_AllowIntersectionsSubject;
}
if (args["allow-intersect-both"]) {
opts |= fCompart_AllowIntersectionsBoth;
}
list< CRef<CSeq_align_set> > compartments;
FindCompartments(aligns, compartments, opts);
LOG_POST(Error << "input alignments: " << aligns.size());
LOG_POST(Error << "output compartments: " << compartments.size());
size_t count = 0;
NON_CONST_ITERATE (list< CRef<CSeq_align_set> >, i, compartments) {
++count;
CSeq_align align;
align.SetSegs().SetDisc(**i);
TSeqRange r1 = align.GetSeqRange(0);
TSeqRange r2 = align.GetSeqRange(1);
CSeq_id_Handle id1 = CSeq_id_Handle::GetHandle(align.GetSeq_id(0));
CSeq_id_Handle id2 = CSeq_id_Handle::GetHandle(align.GetSeq_id(1));
LOG_POST(Error << "compartment " << count << ":");
LOG_POST(Error << " query = " << id1 << " (" << r1.GetFrom() + 1 << ".." << r1.GetTo() + 1 << ")");
LOG_POST(Error << " subject = " << id2 << " (" << r2.GetFrom() + 1 << ".." << r2.GetTo() + 1 << ")");
LOG_POST(Error << " alignments = " << (*i)->Get().size());
string title("Compartment ");
title += NStr::NumericToString(count);
CSeq_annot annot;
annot.SetNameDesc(title);
annot.SetTitleDesc(title);
annot.SetData().SetAlign() = (*i)->Get();
ostr << MSerial_AsnText << annot;
}
CAlignSort::SSortKey
CAlignSort::SAlignExtractor::operator()(const CSeq_align& align)
{
SSortKey key;
ITERATE (vector<string>, iter, key_toks) {
SSortKey::TItem item;
if (NStr::EqualNocase(*iter, "query")) {
CSeq_id_Handle idh =
CSeq_id_Handle::GetHandle(align.GetSeq_id(0));
idh = sequence::GetId(idh, *scope,
sequence::eGetId_Canonical);
item.first = idh.GetSeqId()->AsFastaString();
}
else if (NStr::EqualNocase(*iter, "subject")) {
CSeq_id_Handle idh =
CSeq_id_Handle::GetHandle(align.GetSeq_id(1));
idh = sequence::GetId(idh, *scope,
sequence::eGetId_Canonical);
item.first = idh.GetSeqId()->AsFastaString();
}
else if (NStr::EqualNocase(*iter, "query_start")) {
item.second = align.GetSeqStart(0);
}
else if (NStr::EqualNocase(*iter, "subject_start")) {
item.second = align.GetSeqStart(1);
}
else if (NStr::EqualNocase(*iter, "query_end")) {
item.second = align.GetSeqStop(0);
}
else if (NStr::EqualNocase(*iter, "subject_end")) {
item.second = align.GetSeqStop(1);
}
else if (NStr::EqualNocase(*iter, "query_strand")) {
item.second = align.GetSeqStrand(0);
}
else if (NStr::EqualNocase(*iter, "subject_strand")) {
item.second = align.GetSeqStrand(1);
}
else if (NStr::EqualNocase(*iter, "query_align_len")) {
item.second = align.GetSeqRange(0).GetLength();
}
else if (NStr::EqualNocase(*iter, "subject_align_len")) {
item.second = align.GetSeqRange(1).GetLength();
}
else if (NStr::EqualNocase(*iter, "query_traceback")) {
CScoreBuilder builder;
item.first = builder.GetTraceback(*scope, align, 0);
}
else if (NStr::EqualNocase(*iter, "subject_traceback")) {
CScoreBuilder builder;
item.first = builder.GetTraceback(*scope, align, 1);
}
else {
/// assume it is a score
CScoreLookup lookup;
lookup.SetScope(*scope);
item.second = lookup.GetScore(align, *iter);
}
key.items.push_back(item);
}
MasterSlaveAlignment::MasterSlaveAlignment(
const SequenceSet *sequenceSet,
const Sequence *masterSequence,
const CSeq_align& seqAlign) :
status(CAV_ERROR_PAIRWISE), master(masterSequence), slave(NULL)
{
// resize alignment and block vector
masterToSlave.resize(master->Length(), -1);
SequenceSet::SequenceList::const_iterator
s = sequenceSet->sequences.begin(),
se = sequenceSet->sequences.end();
// find slave sequence for this alignment, and order (master or slave first)
const SeqIdList& sids = seqAlign.GetSegs().IsDendiag() ?
seqAlign.GetSegs().GetDendiag().front()->GetIds() :
seqAlign.GetSegs().GetDenseg().GetIds();
bool masterFirst = true;
for (; s!=se; ++s) {
if ((*s)->Matches(master->bioseqASN->GetId())) continue;
if ((*s)->Matches(sids.back().GetObject())) {
break;
} else if ((*s)->Matches(sids.front().GetObject())) {
masterFirst = false;
break;
}
}
if (s == se) {
// special case of master seq. aligned to itself
if (master->Matches(sids.back().GetObject()) && master->Matches(sids.front().GetObject())) {
slave = master;
} else {
ERR_POST_X(9, Error << "MasterSlaveAlignment::MasterSlaveAlignment() - \n"
"couldn't find matching unaligned slave sequence");
return;
}
} else {
slave = *s;
}
unsigned int i;
int masterRes, slaveRes;
// unpack dendiag alignment
if (seqAlign.GetSegs().IsDendiag()) {
CSeq_align::C_Segs::TDendiag::const_iterator d , de = seqAlign.GetSegs().GetDendiag().end();
for (d=seqAlign.GetSegs().GetDendiag().begin(); d!=de; ++d) {
const CDense_diag& block = d->GetObject();
if (!block.IsSetDim() || block.GetDim() != 2 ||
block.GetIds().size() != 2 ||
block.GetStarts().size() != 2) {
ERR_POST_X(10, Error << "MasterSlaveAlignment::MasterSlaveAlignment() - \n"
"incorrect dendiag block dimensions");
return;
}
// make sure identities of master and slave sequences match in each block
if ((masterFirst &&
(!master->Matches(block.GetIds().front().GetObject()) ||
!slave->Matches(block.GetIds().back().GetObject()))) ||
(!masterFirst &&
(!master->Matches(block.GetIds().back().GetObject()) ||
!slave->Matches(block.GetIds().front().GetObject())))) {
ERR_POST_X(11, Error << "MasterSlaveAlignment::MasterSlaveAlignment() - \n"
"mismatched Seq-id in dendiag block");
return;
}
// finally, actually unpack the data into the alignment vector
for (i=0; i<block.GetLen(); ++i) {
if (masterFirst) {
masterRes = block.GetStarts().front() + i;
slaveRes = block.GetStarts().back() + i;
} else {
masterRes = block.GetStarts().back() + i;
slaveRes = block.GetStarts().front() + i;
}
if (masterRes >= (int) master->Length() || slaveRes >= (int) slave->Length()) {
ERR_POST_X(12, Critical << "MasterSlaveAlignment::MasterSlaveAlignment() - \n"
"seqloc in dendiag block > length of sequence!");
return;
}
masterToSlave[masterRes] = slaveRes;
}
}
}
// unpack denseg alignment
else if (seqAlign.GetSegs().IsDenseg()) {
const CDense_seg& block = seqAlign.GetSegs().GetDenseg();
if (!block.IsSetDim() || block.GetDim() != 2 ||
block.GetIds().size() != 2 ||
block.GetStarts().size() != ((unsigned int ) 2 * block.GetNumseg()) ||
block.GetLens().size() != ((unsigned int ) block.GetNumseg()))
{
ERR_POST_X(13, Error << "MasterSlaveAlignment::MasterSlaveAlignment() - \n"
"incorrect denseg block dimension");
return;
}
// make sure identities of master and slave sequences match in each block
if ((masterFirst &&
(!master->Matches(block.GetIds().front().GetObject()) ||
!slave->Matches(block.GetIds().back().GetObject()))) ||
(!masterFirst &&
(!master->Matches(block.GetIds().back().GetObject()) ||
!slave->Matches(block.GetIds().front().GetObject())))) {
ERR_POST_X(14, Error << "MasterSlaveAlignment::MasterSlaveAlignment() - \n"
"mismatched Seq-id in denseg block");
return;
}
// finally, actually unpack the data into the alignment vector
CDense_seg::TStarts::const_iterator starts = block.GetStarts().begin();
CDense_seg::TLens::const_iterator lens, le = block.GetLens().end();
for (lens=block.GetLens().begin(); lens!=le; ++lens) {
if (masterFirst) {
masterRes = *(starts++);
slaveRes = *(starts++);
} else {
slaveRes = *(starts++);
masterRes = *(starts++);
}
if (masterRes != -1 && slaveRes != -1) { // skip gaps
if ((masterRes + *lens - 1) >= master->Length() ||
(slaveRes + *lens - 1) >= slave->Length()) {
ERR_POST_X(15, Critical << "MasterSlaveAlignment::MasterSlaveAlignment() - \n"
"seqloc in denseg block > length of sequence!");
return;
}
for (i=0; i<*lens; ++i)
masterToSlave[masterRes + i] = slaveRes + i;
}
}
}
status = CAV_SUCCESS;
}
