CRef<CSeq_entry>
CShortReadFastaInputSource::x_ReadFastaOneSeq(CRef<ILineReader> line_reader)
{
int start = 0;
// parse the last read defline
CTempString line = **line_reader;
CTempString id = x_ParseDefline(line);
CRef<CSeq_id> seqid(new CSeq_id);
seqid->Set(CSeq_id::e_Local, id);
++(*line_reader);
line = **line_reader;
while (line[0] != '>') {
// ignore empty lines
if (line.empty() && !line_reader->AtEOF()) {
++(*line_reader);
line = **line_reader;
continue;
}
// copy the sequence
// increase the sequence buffer if necessary
if (start + line.length() + 1 > m_SeqBuffLen) {
string tmp;
m_SeqBuffLen = 2 * (start + line.length() + 1);
tmp.reserve(m_SeqBuffLen);
memcpy(&tmp[0], &m_Sequence[0], start);
m_Sequence.swap(tmp);
}
memcpy(&m_Sequence[start], line.data(), line.length());
start += line.length();
if (line_reader->AtEOF()) {
break;
}
// read next line
++(*line_reader);
line = **line_reader;
}
// set up sequence
if (start > 0) {
CRef<CSeq_entry> seq_entry(new CSeq_entry);
CBioseq& bioseq = seq_entry->SetSeq();
bioseq.SetInst().SetMol(CSeq_inst::eMol_na);
bioseq.SetInst().SetRepr(CSeq_inst::eRepr_raw);
bioseq.SetId().clear();
bioseq.SetId().push_back(seqid);
bioseq.SetInst().SetLength(start);
m_Sequence[start] = 0;
bioseq.SetInst().SetSeq_data().SetIupacna(CIUPACna(&m_Sequence[0]));
bioseq.SetDescr();
m_BasesAdded += start;
return seq_entry;
}
return CRef<CSeq_entry>();
}
void CSeq_data::DoConstruct(const string& value, E_Choice index)
{
switch (index) {
case e_Iupacna:
SetIupacna() = CIUPACna(value);
break;
case e_Iupacaa:
SetIupacaa() = CIUPACaa(value);
break;
case e_Ncbieaa:
SetNcbieaa() = CNCBIeaa(value);
break;
default:
// throw an error
NCBI_THROW (CException, eUnknown,
"CSeq_data::DoConstruct: Invalid E_Choice index");
}
}
CRef<CSeq_entry>
CShortReadFastaInputSource::x_ReadFastqOneSeq(CRef<ILineReader> line_reader)
{
CTempString line;
CTempString id;
CRef<CSeq_entry> retval;
// first read defline
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
if (line[0] != '@') {
NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:"
" defline expected at line: " +
NStr::IntToString(line_reader->GetLineNumber()));
}
id = x_ParseDefline(line);
CRef<CSeq_id> seqid(new CSeq_id);
seqid->Set(CSeq_id::e_Local, id);
// read sequence
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
// set up sequence
if (line.length() > 0) {
CRef<CSeq_entry> seq_entry(new CSeq_entry);
CBioseq& bioseq = seq_entry->SetSeq();
bioseq.SetInst().SetMol(CSeq_inst::eMol_na);
bioseq.SetInst().SetRepr(CSeq_inst::eRepr_raw);
bioseq.SetId().clear();
bioseq.SetId().push_back(seqid);
bioseq.SetInst().SetLength(line.length());
bioseq.SetInst().SetSeq_data().SetIupacna(CIUPACna(line.data()));
bioseq.SetDescr();
m_BasesAdded += line.length();
retval = seq_entry;
}
// read and skip second defline
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
if (line[0] != '+') {
NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:"
" defline expected at line: " +
NStr::IntToString(line_reader->GetLineNumber()));
}
// read and skip quality scores
++(*line_reader);
line = **line_reader;
// skip empty lines
while (!line_reader->AtEOF() && line.empty()) {
++(*line_reader);
line = **line_reader;
}
return retval;
}
void
CShortReadFastaInputSource::x_ReadFastc(CBioseq_set& bioseq_set,
TSeqPos batch_size)
{
string id;
// tags to indicate paired sequences
CRef<CSeqdesc> seqdesc_first(new CSeqdesc);
seqdesc_first->SetUser().SetType().SetStr("Mapping");
seqdesc_first->SetUser().AddField("has_pair", eFirstSegment);
CRef<CSeqdesc> seqdesc_last(new CSeqdesc);
seqdesc_last->SetUser().SetType().SetStr("Mapping");
seqdesc_last->SetUser().AddField("has_pair", eLastSegment);
m_BasesAdded = 0;
while (m_BasesAdded < batch_size && !m_LineReader->AtEOF()) {
++(*m_LineReader);
m_Line = **m_LineReader;
// ignore empty lines
if (m_Line.empty()) {
continue;
}
// if defline
if (m_Line[0] == '>') {
id = x_ParseDefline(m_Line);
}
else {
// otherwise sequence
// make sure that a defline was read first
if (id.empty()) {
NCBI_THROW(CInputException, eInvalidInput,
(string)"Missing defline before line: " +
NStr::IntToString(m_LineReader->GetLineNumber()));
}
// find '><' that separate reads of a pair
size_t p = m_Line.find('>');
if (p == CTempString::npos || m_Line[p + 1] != '<') {
NCBI_THROW(CInputException, eInvalidInput,
(string)"FASTC parse error: Sequence separator '><'"
" was not found in line: " +
NStr::IntToString(m_LineReader->GetLineNumber()));
}
// set up reads, there are two sequences in the same line separated
char* first = (char*)m_Line.data();
char* second = (char*)m_Line.data() + p + 2;
size_t first_len = p;
size_t second_len = m_Line.length() - p - 2;
{{
CRef<CSeq_id> seqid(new CSeq_id);
seqid->Set(CSeq_id::e_Local, id + ".1");
CRef<CSeq_entry> seq_entry(new CSeq_entry);
CBioseq& bioseq = seq_entry->SetSeq();
bioseq.SetInst().SetMol(CSeq_inst::eMol_na);
bioseq.SetInst().SetRepr(CSeq_inst::eRepr_raw);
bioseq.SetId().clear();
bioseq.SetId().push_back(seqid);
bioseq.SetInst().SetLength(first_len);
first[first_len] = 0;
bioseq.SetInst().SetSeq_data().SetIupacna(CIUPACna(first));
bioseq.SetDescr().Set().push_back(seqdesc_first);
// add a sequence to the batch
bioseq_set.SetSeq_set().push_back(seq_entry);
}}
{{
CRef<CSeq_id> seqid(new CSeq_id);
seqid->Set(CSeq_id::e_Local, id + ".2");
CRef<CSeq_entry> seq_entry(new CSeq_entry);
CBioseq& bioseq = seq_entry->SetSeq();
bioseq.SetInst().SetMol(CSeq_inst::eMol_na);
bioseq.SetInst().SetRepr(CSeq_inst::eRepr_raw);
bioseq.SetId().clear();
bioseq.SetId().push_back(seqid);
bioseq.SetInst().SetLength(second_len);
second[second_len] = 0;
bioseq.SetInst().SetSeq_data().SetIupacna(CIUPACna(second));
bioseq.SetDescr().Set().push_back(seqdesc_last);
// add a sequence to the batch
bioseq_set.SetSeq_set().push_back(seq_entry);
}}
m_BasesAdded += first_len + second_len;
id.clear();
}
}
}
//
// CreateConsensus()
//
// compute a consensus sequence given a particular alignment
// the rules for a consensus are:
// - a segment is consensus gap if > 50% of the sequences are gap at this
// segment. 50% exactly is counted as sequence
// - for a segment counted as sequence, for each position, the most
// frequently occurring base is counted as consensus. in the case of
// a tie, the consensus is considered muddied, and the consensus is
// so marked
//
CRef<CDense_seg>
CAlnVec::CreateConsensus(int& consensus_row, CBioseq& consensus_seq,
const CSeq_id& consensus_id) const
{
consensus_seq.Reset();
if ( !m_DS || m_NumRows < 1) {
return CRef<CDense_seg>();
}
bool isNucleotide = GetBioseqHandle(0).IsNucleotide();
size_t i;
size_t j;
// temporary storage for our consensus
vector<string> consens(m_NumSegs);
CreateConsensus(consens);
//
// now, create a new CDense_seg
// we create a new CBioseq for our data and
// copy the contents of the CDense_seg
//
string data;
TSignedSeqPos total_bases = 0;
CRef<CDense_seg> new_ds(new CDense_seg());
new_ds->SetDim(m_NumRows + 1);
new_ds->SetNumseg(m_NumSegs);
new_ds->SetLens() = m_Lens;
new_ds->SetStarts().reserve(m_Starts.size() + m_NumSegs);
if ( !m_Strands.empty() ) {
new_ds->SetStrands().reserve(m_Strands.size() +
m_NumSegs);
}
for (i = 0; i < consens.size(); ++i) {
// copy the old entries
for (j = 0; j < (size_t)m_NumRows; ++j) {
int idx = i * m_NumRows + j;
new_ds->SetStarts().push_back(m_Starts[idx]);
if ( !m_Strands.empty() ) {
new_ds->SetStrands().push_back(m_Strands[idx]);
}
}
// add our new entry
// this places the consensus as the last sequence
// it should preferably be the first, but this would mean adjusting
// the bioseq handle and seqvector caches, and all row numbers would
// shift
if (consens[i].length() != 0) {
new_ds->SetStarts().push_back(total_bases);
} else {
new_ds->SetStarts().push_back(-1);
}
if ( !m_Strands.empty() ) {
new_ds->SetStrands().push_back(eNa_strand_unknown);
}
total_bases += consens[i].length();
data += consens[i];
}
// copy our IDs
for (i = 0; i < m_Ids.size(); ++i) {
new_ds->SetIds().push_back(m_Ids[i]);
}
// now, we construct a new Bioseq
{{
// sequence ID
CRef<CSeq_id> id(new CSeq_id());
id->Assign(consensus_id);
consensus_seq.SetId().push_back(id);
new_ds->SetIds().push_back(id);
// add a description for this sequence
CSeq_descr& desc = consensus_seq.SetDescr();
CRef<CSeqdesc> d(new CSeqdesc);
desc.Set().push_back(d);
d->SetComment("This is a generated consensus sequence");
// the main one: Seq-inst
CSeq_inst& inst = consensus_seq.SetInst();
inst.SetRepr(CSeq_inst::eRepr_raw);
inst.SetMol(isNucleotide ? CSeq_inst::eMol_na : CSeq_inst::eMol_aa);
inst.SetLength(data.length());
CSeq_data& seq_data = inst.SetSeq_data();
if (isNucleotide) {
CIUPACna& na = seq_data.SetIupacna();
na = CIUPACna(data);
} else {
CIUPACaa& aa = seq_data.SetIupacaa();
aa = CIUPACaa(data);
}
}}
consensus_row = new_ds->GetIds().size() - 1;
return new_ds;
}