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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/compart_8cpp_source.html below:

NCBI C++ ToolKit: src/app/compart/compart.cpp Source File

51 "Compart v.1.35. Unless -qdb and -sdb are specified, " 52 "the tool expects tabular blast hits at stdin collated " 53 "by query and subject, e.g. with 'sort -k 1,1 -k 2,2'"

);

55

argdescr->AddOptionalKey (

"qdb"

"cDNA BLAST database"

58

argdescr->AddOptionalKey (

"sdb"

"Genomic BLAST database"

61

argdescr->AddFlag (

"ho"

"Print raw hits only - no compartments"

);

63

argdescr->AddDefaultKey(

"penalty"

"Per-compartment penalty"

66

argdescr->AddDefaultKey(

"min_idty"

"Minimal overall identity. Note: in current implementation there is no sense to set different 'min_idty' and 'min_singleton_idty' (minimum is used anyway)."

69

argdescr->AddDefaultKey(

"min_singleton_idty"

70 "Minimal identity for singleton compartments. " 71 "The actual parameter passed to the compartmentization " 72 "procedure is least of this parameter multipled " 73 "by the seq length, and min_singleton_idty_bps. Note: in current implementation there is no sense to set different 'min_idty' and 'min_singleton_idty' (minimum is used anyway)."

76

argdescr->AddDefaultKey(

"min_singleton_idty_bps"

77 "Minimal identity for singleton compartments " 78 "in base pairs. Default = parameter disabled."

81

argdescr->AddDefaultKey (

"max_intron"

82 "Maximum intron length (in base pairs)"

87

argdescr->AddDefaultKey(

"dropoff"

88 "Max score drop-off during hit extension."

91

s_GetDefaultDropOff()));

93

argdescr->AddDefaultKey(

"min_query_len"

94 "Minimum length for individual cDNA sequences."

97

argdescr->AddDefaultKey(

"min_hit_len"

98 "Minimum length for reported hits in hits-only mode. " 99 "No effect in compartments mode."

102

argdescr->AddDefaultKey (

"maxvol"

103 "Maximum index volume size in MB (approximate)"

107

argdescr->AddFlag(

"noxf"

"[With external hits] Suppress overlap x-filtering: " 108 "print all compartment hits intact."

);

110

argdescr->AddOptionalKey(

"seqlens"

111 "[With external hits] Two-column file with sequence IDs " 112 "and their lengths. If none supplied, the program will " 113 "attempt fetching the lengths from GenBank. " 114 "Cannot be used with -qdb."

117

argdescr->AddDefaultKey(

"N"

118 "[With external hits] Max number of compartments " 119 "per query (0 = All)."

123

argdescr->SetConstraint(

"penalty"

, constrain01);

124

argdescr->SetConstraint(

"min_idty"

, constrain01);

125

argdescr->SetConstraint(

"min_singleton_idty"

, constrain01);

128

argdescr->SetConstraint(

"maxvol"

, constrain_maxvol);

131

argdescr->SetConstraint(

"min_query_len"

, constrain_minqlen);

134

argdescr->SetConstraint(

"min_hit_len"

, constrain_minhitlen);

146 if

(

id

size

() &&

id

[0] !=

'#'

) {

189 const bool

is_qdb (args[

"qdb"

]);

190 const bool

is_seqlens (args[

"seqlens"

]);

208 m_penalty

= args[

"penalty"

].AsDouble();

268

args[

"sdb"

].AsString()));

270

matcher->SetOutputMethod(

true

);

279

matcher->SetHitsOnly(args[

"ho"

]);

280

matcher->SetMinHitLength(args[

"min_hit_len"

].AsInteger());

281

matcher->SetMaxVolSize(1024 * 1024 * (args[

"maxvol"

].AsInteger()));

283

matcher->SetDropOff(args[

"dropoff"

].AsInteger());

285 try

{ matcher->Run(); }

286 catch

(std::bad_alloc&) {

288 "Not enough memory available to run this program"

);

318 string

query0, subj0;

327 const string query

(hit->GetQueryId()->GetSeqIdString(

true

));

328 const string

subj (hit->GetSubjId()->GetSeqIdString(

true

));

330 if

(query0.size() == 0 || subj0.size() == 0) {

333

id2id[query0] = subj0;

337 if

(

query

!= query0 || subj != subj0) {

340 if

(rv != 0)

return

rv;

342 if

(

query

!= query0) {

352

cout << **ii << endl;

363

TIdToId::const_iterator im = id2id.find(query0);

364 if

(im == id2id.end() || im->second != subj0) {

365

id2id[query0] = subj0;

368

cerr <<

"Input hit stream not properly ordered"

<< endl;

374

hitrefs.push_back(hit);

378 if

(hitrefs.size()) {

380 if

(rv != 0)

return

rv;

388

cout << **ii << endl;

402

cerr <<

"Cannot retrieve sequence lengths for: " 412 typedef

TAccessor::TCoord TCoord;

414 const

TCoord penalty_bps (TCoord(

m_penalty

* qlen + 0.5));

415 const

TCoord min_matches (TCoord(

m_min_idty

* qlen + 0.5));

418 const

TCoord min_singleton_matches (

min

(msm1, msm2));

420

TAccessor ca (penalty_bps, min_matches, min_singleton_matches, !

m_NoXF

);

421

ca.SetMaxIntron(

static_cast<

TCoord

>

(

m_max_intron

));

422

ca.Run(hitrefs.begin(), hitrefs.end());

425 for

(

bool

b0 (ca.GetFirst(comp)); b0 ; b0 = ca.GetNext(comp)) {

440 #ifdef PCOMPARTMENT_RANKER_M1 442 const size_t

exons_lhs (lhs->GetExonCount());

443 const size_t

exons_rhs (rhs->GetExonCount());

444 if

(exons_lhs == exons_rhs) {

445 return

lhs->GetMatchCount() > rhs->GetMatchCount();

448 return

exons_lhs > exons_rhs;

453 const size_t

idtybin_lhs (lhs->GetIdentityBin());

454 const size_t

idtybin_rhs (rhs->GetIdentityBin());

455 if

(idtybin_lhs == idtybin_rhs) {

456 const size_t

exons_lhs (lhs->GetExonCount());

457 const size_t

exons_rhs (rhs->GetExonCount());

458 if

(exons_lhs == exons_rhs) {

459 return

lhs->GetMatchCount() > rhs->GetMatchCount();

462 return

exons_lhs > exons_rhs;

466 return

idtybin_lhs > idtybin_rhs;

470 #undef PCOMPARTMENT_RANKER_M1 519

m_SeqLength(length), m_IdentityBin(0), m_ExonCount(0), m_MatchCount(0)

521 if

(hitrefs.size() == 0) {

523 "Cannot init compartment with empty hit list"

);

526 for

(THitRefs::const_reverse_iterator ii(hitrefs.rbegin()), ie(hitrefs.rend());

535 if

(m_HitRefs.size() == 0) {

536

m_HitRefs.push_back(hitref);

540 const THitRef

& hb (m_HitRefs.back());

541 const bool

cs (hb->GetSubjStrand());

542 if

(cs != hitref->GetSubjStrand()) {

544 "different from that of the compartment."

);

547

m_HitRefs.push_back(hitref);

554 if

(m_HitRefs.size()) {

555 return

m_HitRefs.front()->GetSubjStrand();

565 const THit::TId

& subjid_lhs (m_HitRefs.front()->GetSubjId());

567 const TIntId

co (subjid_lhs->CompareOrdered(*subjid_rhs));

570 const THit::TId

& queryid_lhs (m_HitRefs.front()->GetQueryId());

572 const TIntId

co (queryid_lhs->CompareOrdered(*queryid_rhs));

577 const bool

strand_rhs (rhs.

GetStrand

());

578 if

(strand_lhs == strand_rhs) {

580 return

GetSpan().first < rhs.

GetSpan

().first;

583 return

GetSpan().first > rhs.

GetSpan

().first;

587 return

strand_lhs < strand_rhs;

613 const size_t

kMinIntronLength (25);

614 const size_t

kMinExonLength (10);

617 THitRef

& h (m_HitRefs.front());

618 double

matches ( h->GetLength() * h->GetIdentity() );

620 if

(m_HitRefs.size() > 1) {

628 if

(

.NotEmpty()) {

631 if

(q0 + kMinExonLength <= h->GetQueryStop()) {

634

- (h->GetQueryStart() - q0));

635 if

(

->GetSubjStop() + kMinIntronLength <= s0) {

639

matches += (h->GetQueryStop() - q0max) * h->GetIdentity();

651 if

(

.NotEmpty()) {

654 if

(q0 + kMinExonLength <= h->GetQueryStop()) {

657

+ h->GetQueryStart() - q0);

658 if

(s0 + kMinIntronLength <= prev->GetSubjStop()) {

662

matches += (h->GetQueryStop() - q0max) * h->GetIdentity();

671

m_MatchCount = size_t(

round

(matches));

672

m_IdentityBin = size_t(floor(

double

(m_MatchCount) / m_SeqLength / 0.1));

679

ostr << **ii << endl;

690 int main

(

int

argc,

const char

* argv[])

CCompartment(const THitRefs &hitrefs, size_t length)

bool GetStrand(void) const

void x_AddHit(const THitRef &hitref)

bool operator<(const CCompartment &rhs) const

pair< THit::TCoord, THit::TCoord > TRange

TRange GetSpan(void) const

virtual void Init()

Initialize the application.

CRef< objects::CScope > m_Scope

virtual void Exit()

Cleanup on application exit.

void x_RankAndStore(void)

virtual int Run()

Run the application.

size_t x_GetSeqLength(const string &id)

size_t m_MaxCompsPerQuery

size_t m_min_singleton_idty_bps

TCompartRefs m_Compartments

vector< TCompartRef > TCompartRefs

TCompartRefs m_CompartmentsPermanent

int x_DoWithExternalHits(void)

double m_min_singleton_idty

int x_ProcessPair(const string &query0, THitRefs &hitrefs)

vector< THitRef > THitRefs

void x_ReadSeqLens(CNcbiIstream &istr)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

ostream & operator<<(ostream &ostr, const CCompartApp::CCompartment &rhs)

int main(int argc, const char *argv[])

bool PCompartmentRanker(const CCompartApp::TCompartRef &lhs, const CCompartApp::TCompartRef &rhs)

bool operator<(const CCompartApp::TCompartRef &lhs, const CCompartApp::TCompartRef &rhs)

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fHideLogfile

Hide log file description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

@ eInputFile

Name of file (must exist and be readable)

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

#define NCBI_THROW(exception_class, err_code, message)

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

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

TObjectType * GetNonNullPointer(void)

Get pointer value and throw a null pointer exception if pointer is null.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define USING_SCOPE(ns)

Use the specified namespace.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

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

Convert int to string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

const struct ncbi::grid::netcache::search::fields::SIZE size

#define GetProgramName

Avoid name clash with the NCBI C Toolkit.

std::istream & in(std::istream &in_, double &x_)

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