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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/gtf__writer_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/writers/gtf_writer.cpp Source File

75 unsigned int

uFlags ) :

85 unsigned int

uFlags ) :

104 const auto

& display_range =

GetRange

();

105 CFeat_CI

feat_iter(bsh, display_range, sel);

108

vector<CMappedFeat> vRoots = fc.

FeatTree

().GetRootFeatures();

110 for

(

auto

pit = vRoots.begin(); pit != vRoots.end(); ++pit) {

127 m_Os

"#gtf-version 2.2"

'\n'

;

167 "Processing terminated by user"

);

210

list<CRef<CGtfRecord>> records;

215 for

(

const auto

& record: records) {

227 const string

& transcriptIdPreAssigned)

230 string

transcriptId(transcriptIdPreAssigned);

239

tf =

context

.FeatTree().GetParent(mf);

244

transcriptId = featIt->second;

247

list<CRef<CGtfRecord>> records;

252 for

(

const auto

& record: records) {

264 const string

& transcriptIdPreAssigned )

267 string

transcriptId(transcriptIdPreAssigned);

269

list<CRef<CGtfRecord>> records;

273 for

(

const auto

& record: records) {

293 bool

needsPartNumbers = (sublocs.size() > 1);

294 unsigned int

partNum = 1;

295 for

(

auto

it = sublocs.begin(); it != sublocs.end(); it++ ) {

303

pRecord->SetEndpoints(intv.

GetFrom

(), intv.

GetTo

(), strand);

304 if

(needsPartNumbers) {

305

pRecord->SetPartNumber(partNum++);

307

recordList.push_back(pRecord);

318 const string

& transcriptId)

327 if

(!transcriptId.empty()) {

328

pRecord->SetTranscriptId(transcriptId);

340

mfLocAsPackedInt.

Assign

(mfLoc);

346 if

(isTransSpliced) {

347 auto

rnaStart = sublocs.front()->GetFrom();

348 auto

rnaStop = sublocs.front()->GetTo();

349 for

(

const auto

& loc : sublocs) {

350 auto

start = loc->GetFrom();

351 if

(start < rnaStart) {

354 auto

stop = loc->GetTo();

355 if

(stop > rnaStop) {

359

pRecord->SetEndpoints(rnaStart, rnaStop, mfStrand);

362 TSeqPos

lastFrom = sublocs.front()->GetFrom();

363 TSeqPos

lastTo = sublocs.front()->GetTo();

364 auto

it = sublocs.begin();

365 bool

iterationDone(

false

);

366 for

( it++; it != sublocs.end() && !iterationDone; it++ ) {

371 if

(intv.

GetTo

() <= lastFrom) {

375

pRecord->SetEndpoints(lastFrom, lastTo, mfLoc.GetStrand());

376

recordList.push_back(pRecord);

378 if

(!transcriptId.empty()) {

379

pRecord->SetTranscriptId(transcriptId);

385

lastTo = intv.

GetTo

();

393

iterationDone =

true

;

398 if

(intv.

GetFrom

() >= lastTo) {

399

lastTo = intv.

GetTo

();

402

pRecord->SetEndpoints(lastFrom, lastTo, mfLoc.GetStrand());

403

recordList.push_back(pRecord);

405 if

(!transcriptId.empty()) {

406

pRecord->SetTranscriptId(transcriptId);

412

lastTo = intv.

GetTo

();

418

pRecord->SetEndpoints(lastFrom, lastTo, mfLoc.GetStrand());

420

recordList.push_back(pRecord);

422 bool

needPartNumbers = (recordList.size() > 1);

423 unsigned int

partNum = 1;

424 for

(

auto

& record: recordList) {

425 if

(needPartNumbers) {

426

record->SetPartNumber(partNum++);

428

record->SetType(

"transcript"

);

429

record->SetGbKeyFrom(mf);

439 const string

& parentTranscriptId)

442 string

transcriptId(parentTranscriptId);

447

mfLocAsPackedInt.

Assign

(mfLoc);

455 if

(cdsFeat.GetData().GetCdregion().IsSetFrame()) {

456

phase =

max

(cdsFeat.GetData().GetCdregion().GetFrame()-1, 0);

459 unsigned int

partNum = 1;

460 for

(

auto

pInterval : sublocs) {

468

pRecord->SetEndpoints(intv.

GetFrom

(), intv.

GetTo

(), strand);

469 if

(needsPartNumbers) {

472 if

(!transcriptId.empty()) {

473

pRecord->SetTranscriptId(transcriptId);

476

transcriptId = pRecord->TranscriptId();

478

pRecord->SetCdsPhase(phase);

479

recordList.push_back(pRecord);

480

phase = (3 - ((intv.

GetLength

()+3 - phase)%3))%3;

484 unsigned int

basesToLose = 3;

485 while

(basesToLose > 0 && !recordList.empty()) {

486 auto

pLastRecord = recordList.back();

487 auto

lastSize = pLastRecord->SeqStop() - pLastRecord->SeqStart() + 1;

488 auto

lastStrand = pLastRecord->SeqStrand();

489 if

(lastSize > basesToLose) {

491

pLastRecord->SetEndpoints(

492

pLastRecord->SeqStart() + basesToLose, pLastRecord->SeqStop(), lastStrand);

495

pLastRecord->SetEndpoints(

496

pLastRecord->SeqStart(), pLastRecord->SeqStop() - basesToLose, lastStrand);

501

recordList.erase(--recordList.end());

502

basesToLose -= lastSize;

508 int

basePairsNeeded = 3;

509 auto

currentIt = sublocs.begin();

510 unsigned int

partNumber = 1;

511 unsigned int

baseCount = 0;

513 while

(basePairsNeeded > 0 && currentIt != sublocs.end()) {

515 auto

currentFrom = currentLoc.

GetFrom

();

516 auto

currentTo = currentLoc.

GetTo

();

524

pRecord->SetType(

"start_codon"

);

526 if

(currentTo >= currentFrom + basePairsNeeded -1) {

528

pRecord->SetEndpoints(currentTo - basePairsNeeded + 1, currentTo, currentStrand);

531

pRecord->SetEndpoints(currentFrom, currentFrom + basePairsNeeded -1, currentStrand);

536

pRecord->SetEndpoints(currentFrom, currentTo, currentStrand);

537

basePairsNeeded = basePairsNeeded - (currentTo - currentFrom + 1);

540 if

(partNumber > 1 || basePairsNeeded > 0) {

541

pRecord->SetPartNumber(partNumber++);

543 if

(!transcriptId.empty()) {

544

pRecord->SetTranscriptId(transcriptId);

547

pRecord->SetCdsPhase((3-baseCount)%3);

548

baseCount += pRecord->GetExtent();

549

recordList.push_back(pRecord);

556

list<CRef<CGtfRecord>> stopCodonParts;

557 int

basePairsNeeded = 3;

558 auto

currentIt = sublocs.rbegin();

559 while

(basePairsNeeded > 0 && currentIt != sublocs.rend()) {

561 auto

currentFrom = currentLoc.

GetFrom

();

562 auto

currentTo = currentLoc.

GetTo

();

570

pRecord->SetType(

"stop_codon"

);

572 if

(currentTo >= currentFrom + basePairsNeeded - 1) {

574

pRecord->SetEndpoints(currentFrom, currentFrom + basePairsNeeded - 1, currentStrand);

577

pRecord->SetEndpoints(currentTo - basePairsNeeded + 1, currentTo, currentStrand);

582

pRecord->SetEndpoints(currentFrom, currentTo, currentStrand);

583

basePairsNeeded = basePairsNeeded - (currentTo - currentFrom + 1);

586 if

(!transcriptId.empty()) {

587

pRecord->SetTranscriptId(transcriptId);

589

stopCodonParts.push_front(pRecord);

592 unsigned int

partNumber = 1;

593 bool

needPartNumbers = (stopCodonParts.size() > 1);

594 unsigned int

baseCount = 0;

595 for

(

auto

& pRecord: stopCodonParts) {

596 if

(needPartNumbers) {

597

pRecord->SetPartNumber(partNumber++);

600

pRecord->SetCdsPhase((3-baseCount)%3);

601

baseCount += pRecord->GetExtent();

602

recordList.push_back(pRecord);

609 for

(

auto

& pRecord: recordList) {

621 const string

& transcriptId)

625 if

(!transcriptId.empty()) {

626

pMrna->SetTranscriptId(transcriptId);

631

pMrna->CorrectType(

"exon"

);

634 unsigned int

uExonNumber = 1;

637

pLocMrna->

Add

( loc );

643 const

list<CRef<CSeq_interval>>& sublocs = pLocMrna->

GetPacked_int

().

Get

();

644 for

(

auto

it = sublocs.begin(); it != sublocs.end(); ++it) {

648

pExon->MakeChildRecord(*pMrna, subint, uExonNumber++);

649

pExon->DropAttributes(

"gbkey"

);

665 const auto

& quals = mf.

GetQual

();

666 auto

it = quals.begin();

667 for

( ; it != quals.end(); ++it) {

668 if

(!(*it)->CanGetQual() || !(*it)->CanGetVal()) {

671 if

((*it)->GetQual() ==

"standard_name"

) {

672

record.

SetType

((*it)->GetVal());

687

record.

SetType

(

"transcript"

);

713 const auto

& quals = mf.

GetQual

();

714 auto

it = quals.begin();

715 for

(; it != quals.end(); ++it) {

716 if

(!(*it)->CanGetQual() || !(*it)->CanGetVal()) {

719 if

((*it)->GetQual() ==

"gff_source"

) {

728

mf.

GetExt

(),

"ModelEvidence"

);

729 if

(model_evidence) {

731 if

(model_evidence->

HasField

(

"Method"

) ) {

741

mf.

GetExts

(),

"ModelEvidence"

);

742 if

(model_evidence) {

744 if

(model_evidence->

HasField

(

"Method"

)) {

756 if

(!typeFromId.empty()) {

783 const

vector<string> specialCases = {

793 for

(

auto

qual: quals) {

794 if

(!qual->IsSetQual() || !qual->IsSetVal()) {

797 auto

specialCase = std::find(

798

specialCases.begin(), specialCases.end(), qual->GetQual());

799 if

(specialCase != specialCases.end()) {

840 return

featIt->second;

843 auto

parent =

context

.FeatTree().GetParent(mf);

846 return

featIt->second;

849 auto

children =

context

.FeatTree().GetChildren(mf);

850 for

(

auto

child : children) {

853 return

featIt->second;

877 static

list<CSeqFeatData::ESubtype> nonRnaTranscripts = {

888

nonRnaTranscripts.begin(), nonRnaTranscripts.end(), featSubtype);

889 if

(it == nonRnaTranscripts.end()) {

922 switch

(featSubtype) {

965 if

(featId.empty()) {

969 if

(featId.empty()) {

986 unsigned int

suffix = 1;

1009 if

(!record.

GeneId

().empty()) {

1017 const auto

& geneIdQual = mf.

GetNamedQual

(

"gene_id"

);

1018 if

(!geneIdQual.empty()) {

1037 if

(geneId.empty() && geneRef.IsSetLocus_tag()) {

1038

geneId = geneRef.GetLocus_tag();

1040 if

(geneId.empty() && geneRef.IsSetLocus()) {

1041

geneId = geneRef.GetLocus();

1043 if

(geneId.empty() && geneRef.IsSetSyn() ) {

1044

geneId = geneRef.GetSyn().front();

1046 if

(geneId.empty()) {

1064 unsigned int

suffix = 1;

User-defined methods of the data storage class.

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

bool CdsNeedsExonNumbers() const

void AssignExonNumberTo(CGtfRecord &gtfRecord) const

CWriterBase implementation that formats Genbank objects as plain GFF files.

virtual bool xAssignFeatureAttributeDbxref(CGffFeatureRecord &, CGffFeatureContext &, const string &label, const CMappedFeat &)

virtual bool xAssignFeature(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

static bool HasAccaptableTranscriptParent(CGffFeatureContext &, const CMappedFeat &)

virtual bool xWriteAllChildren(CGffFeatureContext &, const CMappedFeat &)

static bool xIntervalsNeedPartNumbers(const list< CRef< CSeq_interval >> &)

CMappedFeat xGenerateMissingTranscript(CGffFeatureContext &, const CMappedFeat &)

virtual string StrType() const

virtual string StrSeqStop() const

virtual string StrAttributes() const

virtual string StrScore() const

void SetType(const string &)

virtual string StrPhase() const

void SetMethod(const string &)

bool SetAttribute(const string &, const string &)

virtual string StrSeqStart() const

virtual string StrSeqId() const

bool AddAttribute(const string &, const string &)

virtual string StrStrand() const

virtual string StrMethod() const

void AssignShouldInheritPseudo(bool shouldInheritPseudo)

feature::CFeatTree & FeatTree()

virtual string StrStructibutes() const

string NextId(const string prefix)

void SetGeneId(const std::string &geneId)

string TranscriptId() const

void SetTranscriptId(const std::string &transcriptId)

virtual bool xAssignFeatureAttributeTranscriptId(CGtfRecord &, CGffFeatureContext &, const CMappedFeat &)

map< CMappedFeat, string > mMapFeatToGeneId

virtual bool xAssignFeaturesGene(list< CRef< CGtfRecord >> &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureMethod(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

virtual bool xWriteRecordsGene(CGffFeatureContext &, const CMappedFeat &)

CGtfIdGenerator mIdGenerator

bool xWriteRecord(const CGffWriteRecord *)

virtual bool xAssignFeaturesCds(list< CRef< CGtfRecord >> &, CGffFeatureContext &, const CMappedFeat &, const string &="")

virtual bool xAssignFeatureAttributeTranscriptBiotype(CGtfRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureAttributeNote(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool xWriteFeature(CGffFeatureContext &, const CMappedFeat &) override

bool x_WriteBioseqHandle(CBioseq_Handle) override

bool xAssignFeatureAttributesFormatSpecific(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

virtual bool xWriteRecordsTranscript(CGffFeatureContext &, const CMappedFeat &, const string &="")

std::string xGenericTranscriptId(const CMappedFeat &)

bool WriteHeader() override

Write a file header identifying the file content as GFF version 2.

CGtfWriter(CScope &, CNcbiOstream &, unsigned int=0)

bool xAssignFeatureAttributesQualifiers(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool xAssignFeatureAttributeDbxref(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

virtual bool xWriteRecordsCds(CGffFeatureContext &, const CMappedFeat &, const string &="")

virtual bool xAssignFeatureAttributeGeneId(CGtfRecord &, CGffFeatureContext &, const CMappedFeat &)

bool xAssignFeatureType(CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

virtual bool xWriteFeatureExons(CGffFeatureContext &, const CMappedFeat &, const string &="")

std::string xGenericGeneId(const CMappedFeat &, CGffFeatureContext &)

virtual bool xAssignFeaturesTranscript(list< CRef< CGtfRecord >> &, CGffFeatureContext &, const CMappedFeat &, const string &)

TSeqPos GetLength(void) const

static bool FeatureToSoType(const CSeq_feat &, string &)

bool HasField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Verify that a named field exists.

const CUser_field & GetField(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

Access a named field in this user object.

static bool CompareFeatures(const CMappedFeat &lhs, const CMappedFeat &rhs)

static CConstRef< CUser_object > GetUserObjectByType(const CUser_object &uo, const string &strType)

static bool GetIdType(CBioseq_Handle, string &)

virtual const CRange< TSeqPos > & GetRange(void) const

bool GetBestId(CSeq_id_Handle idh, CScope &scope, string &best_id) const

virtual SAnnotSelector & SetAnnotSelector(void)

const_iterator end() const

const_iterator find(const key_type &key) const

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

unsigned int TSeqPos

Type for sequence locations and lengths.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void ChangeToPackedInt(void)

Works only if location is currently an interval, point, packed-int (handled trivially),...

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

bool IsSetStrand(EIsSetStrand flag=eIsSetStrand_Any) const

Check if strand is set for any/all part(s) of the seq-loc depending on the flag.

CMappedFeat GetBestGeneForFeat(const CMappedFeat &feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

CMappedFeat GetParentFeature(const CMappedFeat &feat)

CSeq_id_Handle GetIdHandle(const CSeq_loc &loc, CScope *scope)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

bool IsSetExcept(void) const

bool GetExcept(void) const

bool IsSetComment(void) const

const CSeq_feat::TExts & GetExts(void) const

const CSeqFeatData & GetData(void) const

bool IsSetExcept_text(void) const

bool IsSetProduct(void) const

const string & GetComment(void) const

const CUser_object & GetExt(void) const

const string & GetExcept_text(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

bool IsSetExts(void) const

bool IsSetQual(void) const

CSeqFeatData::ESubtype GetFeatSubtype(void) const

CSeqFeatData::E_Choice GetFeatType(void) const

const CSeq_feat::TQual & GetQual(void) const

bool IsSetExt(void) const

CSeq_id_Handle GetProductId(void) const

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

const CSeq_feat & GetMappedFeature(void) const

Feature mapped to the master sequence.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string UIntToString(unsigned int value, TNumToStringFlags flags=0, int base=10)

Convert UInt to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TGene & GetGene(void) const

Get the variant data.

bool IsRna(void) const

Check if variant Rna is selected.

const Tdata & Get(void) const

Get the member data.

TFrom GetFrom(void) const

Get the From member data.

bool IsSetStrand(void) const

Check if a value has been assigned to Strand data member.

bool CanGet(void) const

Check if it is safe to call Get method.

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

const TPacked_int & GetPacked_int(void) const

Get the variant data.

constexpr auto sort(_Init &&init)

static CS_CONTEXT * context

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