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

41  if

( !(*gen_feature)->GetData().IsFtable() )

continue

;

51  if

( !(*f)->GetData().IsGene() )

continue

;

52  string

qname; (*f)->GetData().GetGene().GetLabel(&qname);

53  if

( diag.

find

(qname) == diag.

end

() )

continue

;

69  if

( !(problem->type &

type

) )

continue

;

71  if

(!problem->message.size())

continue

;

82  for

(list<problemStr>::iterator problem = diag[qname].problems.

begin

(); problem!=diag[qname].problems.

end

();)

85  if

( !(problem->type &

type

) )

91

problem=diag[qname].problems.

erase

(problem);

115

qnames[0]=qname1; qnames[1]=qname2;

116  for

(

int i

=0;

i

<2;

i

++)

118  string

& qname = qnames[

i

];

119  if

( diag.

find

(qname) != diag.

end

() )

131  string

qname = problem->first;

132  if

(

done

.find(qname)!=

done

.end())

continue

;

155  ITERATE

(list<problemStr>, problem, diag[qname].problems)

161  if

(problem->type &

type

)

180

strres <<

"unknown_problem_type="

<<

type

<<

'\0'

;

181  string result

=strres.str();

183  result

=

"Potential overlap found"

;

185  result

=

"Potential RNA overlap found"

;

187  result

=

"Complete overlap found"

;

189  result

=

"overlap marked for removal"

;

191  result

=

"Something relevant to frame shift found"

;

193  result

=

"Potential frame shift evidence found"

;

195  result

=

"Evidence absolving from the frame shift accusation found"

;

197  result

=

"Potential partial protein annotation found"

;

199  result

=

"Short annotation found"

;

201  result

=

"tRNA is missing in the list of independently annotated tRNAs"

;

203  result

=

"RNA is missing in the list of annotated RNAs in the input"

;

205  result

=

"RNA is present at the wrong strand"

;

207  result

=

"RNA is present with undefined strand"

;

209  result

=

"tRNA is a complete mismatch"

;

211  result

=

"tRNA has mismatched ends"

;

243  out

<< name.c_str() ;

261  if

(!feat->GetData().IsRna() && !feat->GetData().IsGene())

continue

;

262  const CSeq_loc

& loc = feat->GetLocation();

269  if

(problem_locs.

find

(range)==problem_locs.

end

())

continue

;

271

problem_locs[range].count++;

272  if

(feat->GetData().IsRna()) problem_locs[range].rnacount++;

273  if

(feat->GetData().IsGene()) problem_locs[range].genecount++;

278  if

(!feat->GetData().IsRna() && !feat->GetData().IsGene())

continue

;

280  CSeq_loc

& loc = feat->SetLocation();

285  if

(problem_locs.

find

(range)==problem_locs.

end

())

continue

;

287  if

( problem_locs[range].

count

!=2

288

|| problem_locs[range].rnacount!=1

289

|| problem_locs[range].genecount!=1

294  NcbiCerr

<<

"CReadBlastApp::FixStrands: " 296

<<

"location found, but the number of features with that location is confusing, " 298

<<

"["

<< problem_locs[range].name <<

"]" 299

<<

"("

<< range <<

")" 307

inter->SetStrand(problem_locs[range].strand);

308  NcbiCerr

<<

"CReadBlastApp::FixStrands: " 309

<<

"["

<< problem_locs[range].name <<

"] " 328  for

(CSeq_submit::C_Data::TEntrys::iterator entry =

m_Submit

.

SetData

().SetEntrys().begin();

335

<<

"RemoveProblems(void): doing entry: removeme = " 340  NcbiCerr

<<

"RemoveProblems(): WARNING: " 341

<<

"CSeq_entry deleted, loss of annotation might occur" 357

<<

"RemoveProblems(void): case is single entry " 376

<<

"RemoveProblems(CSeq_entry)(seq case): removeme = " 390

<<

"RemoveProblems(CSeq_entry)(set case): removeme = " 392

<<

", entries.size = " 405  if

(!entry.

IsSet

())

return

;

408  if

(

entries

.size()!=1)

return

;

414  for

(CSeq_descr::Tdata::iterator desc = descs.begin(); desc!=descs.end(); )

416

seq.

SetDescr

().Set().push_back(*desc);

417

desc=descs.erase(desc);

423  NcbiCerr

<<

"NormalizeSeqentry(CSeq_entry...): " 425

<<

"converted sequence set to sequence" 433  bool

noannot=

false

;

439  if

(all_entries_removed > 0) {

; noseqs=

true

;}

444  if

(all_annot_removed > 0) {setseq.

ResetAnnot

(); noannot=

true

;}

446  if

(noseqs ) removeme = 1;

449

<<

"RemoveProblems(CBioseq_set): noseqs = " 453

<<

", removeme (return) = " 477  string

origName = thisName;

478

string::size_type ipos = thisName.rfind(

'|'

);

if

(ipos!=string::npos) thisName.erase(0, ipos+1);

479

ipos = thisName.rfind(

'_'

);

if

(ipos!=string::npos) ipos= thisName.rfind(

'_'

, ipos-1);

482

<<

"RemoveProblems(CBioseq): remove? sequence " 483

<<

"["

<< origName <<

"]" 485

<<

"["

<< thisName <<

"]" 488  if

(problem_seqs.

find

(thisName) != problem_seqs.

end

())

491

<<

"RemoveProblems(CBioseq): sequence " 492

<<

"["

<< origName <<

"]" 493

<<

" is marked for removal, because of a match to " 494

<<

"["

<< thisName <<

"]" 501

<<

"RemoveProblems(CBioseq): remove = " 514  for

(CBioseq_set::TSeq_set::iterator entries_end =

entries

.end(), entry=

entries

.begin(); entry != entries_end; )

519

<<

"RemoveProblems(CBioseq_set::TSeq_set): removeseq = " 523  if

(removeseq) entry=

entries

.erase(entry);

529

<<

"RemoveProblems(CBioseq_set::TSeq_set): nentries = " 541  for

(CBioseq::TAnnot::iterator annot=annots.begin(); annot!=annots.end(); )

544  if

( (*annot)->GetData().IsFtable()) removeme=

RemoveProblems

((*annot)->SetData().SetFtable(), problem_seqs, loc_map);

547  NcbiCerr

<<

"RemoveProblems(annots, problem_seqs): " 549

<<

"annotation has empty feature table and it will be removed" 551

annot=annots.erase(annot);

555  if

(annots.size()==0)

remove

=1;

567  for

(CSeq_annot::C_Data::TFtable::iterator feat_end =

table

.end(), feat =

table

.begin(); feat != feat_end;)

571

gene = (*feat)->GetData().IsGene();

572

cdregion = (*feat)->GetData().IsCdregion();

573  bool

del_feature=

false

;

579  if

(

PrintDetails

())

NcbiCerr

<<

"RemoveProblems(CSeq_annot::C_Data::TFtable): feat: ("

<< real_loc_string <<

")("

<< loc_string <<

")"

<<

NcbiEndl

;

583  if

(problem_seqs.

find

(loc_string) != problem_seqs.

end

())

585  if

((*feat)->GetData().IsImp() &&

586

(*feat)->GetData().GetImp().CanGetKey())

588  NcbiCerr

<<

"RemoveProblems: INFO: feature "

<< loc_string <<

": imp, key = "

<< (*feat)->GetData().GetImp().GetKey() <<

NcbiEndl

;

590  if

((*feat)->GetData().IsImp() &&

591

(*feat)->CanGetComment() )

593  NcbiCerr

<<

"RemoveProblems: INFO: feature "

<< loc_string <<

": imp, comment = "

<< (*feat)->GetComment() <<

NcbiEndl

;

603  if

((*feat)->GetData().IsImp() &&

604

(*feat)->GetData().GetImp().CanGetKey() &&

605

(*feat)->GetData().GetImp().GetKey() ==

"misc_feature" 606

) del_feature =

false

;

607  else

del_feature=

true

;

612  NcbiCerr

<<

"RemoveProblems: feature "

<< loc_string <<

": "

;

613  if

(del_feature)

NcbiCerr

<<

"WILL BE REMOVED"

;

614  else NcbiCerr

<<

"stays until further analysis for it"

;

619  NcbiCerr

<<

"RemoveProblems: WARNING: feature " 620

<<

"{"

<< (*feat)->GetData().SelectionName((*feat)->GetData().Which()) <<

"} " 621

<< loc_string <<

": "

;

622  NcbiCerr

<<

"will be removed because of a problem: "

;

626  if

(!del_feature && gene && (*feat)->GetData().GetGene().CanGetLocus_tag() )

631  string

locus_tag = (*feat)->GetData().GetGene().GetLocus_tag();

632  if

(problem_seqs.

find

(locus_tag) != problem_seqs.

end

()) del_feature=

true

;

635  NcbiCerr

<<

"RemoveProblems: gene "

<< locus_tag <<

": "

;

644  NcbiCerr

<<

"RemoveProblems: WARNING: gene "

<< locus_tag <<

": "

;

645  NcbiCerr

<<

"will be removed because of a problem: "

;

650  if

(!del_feature && cdregion && (*feat)->CanGetProduct() )

656  if

( (*feat)->CanGetProduct() &&

657

(*feat)->GetProduct().IsWhole() &&

658

(*feat)->GetProduct().GetWhole().IsGeneral() &&

659

(*feat)->GetProduct().GetWhole().GetGeneral().CanGetTag() &&

660

(*feat)->GetProduct().GetWhole().GetGeneral().GetTag().IsStr() )

662

productName = (*feat)->GetProduct().GetWhole().GetGeneral().GetTag().GetStr();

665

(*feat)->CanGetProduct() &&

666

(*feat)->GetProduct().IsWhole())

668

productName = (*feat)->GetProduct().GetWhole().AsFastaString();

671

string::size_type ipos=productName.rfind(

'_'

, productName.size());

672  if

(ipos != string::npos)

674

string::size_type ipos2;

675

ipos2=productName.rfind(

'_'

, ipos-1);

676  if

(ipos2 != string::npos) productName.erase(0, ipos2+1);

680

ipos2=productName.rfind(

'|'

, ipos-1);

681  if

(ipos2 != string::npos) productName.erase(0, ipos2+1);

685  if

(productName.length() && problem_seqs.

find

(productName) != problem_seqs.

end

()) del_feature=

true

;

688  NcbiCerr

<<

"RemoveProblems: cdregion "

<< productName <<

": "

;

698  if

(problem_seqs.

find

(real_loc_string) == problem_seqs.

end

())

700

problem_seqs[real_loc_string]=problem_seqs[loc_string];

703  if

(del_feature) feat=

table

.erase(feat);

706  if

(

table

.size()==0) removeme=1;

722  if

(seq->IsSetAnnot() && seq->IsAa()) nremoved+=

RemoveInterim

(seq->SetAnnot());

723  if

(seq->IsSetAnnot() && seq->IsNa()) nremoved+=

RemoveInterim2

(seq->SetAnnot());

736  for

(CBioseq::TAnnot::iterator annot=annots.begin(), annot_end = annots.end(); annot != annot_end; )

738  bool

erased =

false

;

739  if

((*annot)->GetData().IsAlign())

741

nremoved++; erased =

true

;

743  if

( (*annot)->GetData().IsFtable())

747  for

(CSeq_annot::C_Data::TFtable::iterator feat=

table

.begin(), feat_end=

table

.end(); feat != feat_end; )

749  string test

=

"Genomic Location:"

;

750  if

((*feat)->IsSetData() && (*feat)->GetData().IsProt() &&

751

(*feat)->IsSetComment() && (*feat)->GetComment().substr(0,

test

.size()) ==

test

)

753  table

.erase(feat++); dremoved++;

775

<<

", left="

<< (*annot)->GetData().GetFtable().size()

777  if

((*annot)->SetData().SetFtable().size() == 0)

783  if

(erased) annot=annots.erase(annot);

800  if

( !(*gen_feature)->GetData().IsFtable() )

continue

;

804  for

(CSeq_annot::C_Data::TFtable::iterator feat_end =

table

.end(), feat =

table

.begin(); feat != feat_end;)

813  if

(feat_defined.

find

(buff.str()) != feat_defined.

end

())

816

feat=

table

.erase(feat);

821

feat_defined[buff.str()]=

true

;

844 int addProblems

(list<problemStr>& dest,

const

list<problemStr>& src)

847  ITERATE

(list<problemStr>, src_p, src)

849

dest.push_back(*src_p);

859  ITERATE

(list<problemStr>, problem, feat->second.problems)

862  string

name = feat->first;

863

string::size_type ipos = name.rfind(

'|'

);

if

(ipos!=string::npos) name.erase(0, ipos+1);

864

ipos = name.rfind(

'_'

);

if

(ipos!=string::npos) ipos= name.rfind(

'_'

, ipos-1);

865  if

(ipos!=string::npos) name.erase(0, ipos+1);

869

&& !problem->misc_feat_message.empty()

872

problem_locs[range].strand = problem->strand;

873

problem_locs[range].name = name;

874

problem_locs[range].count =

875

problem_locs[range].rnacount =

876

problem_locs[range].genecount = 0;

880  NcbiCerr

<<

"CReadBlastApp::CollectRNAFeatures: "

<< feat->first

881

<<

"["

<< range <<

"]: " 882

<<

"("

<< name <<

")" 883

<< (added ?

"added"

:

"skipped"

) <<

NcbiEndl

;

886  return static_cast<int>

(problem_locs.

size

());

893  bool

keep_frameshifted = args[

"kfs"

].HasValue();

896  ITERATE

(list<problemStr>, problem, feat->second.problems)

899  string

name = feat->first;

900

string::size_type ipos = name.rfind(

'|'

);

if

(ipos!=string::npos) name.erase(0, ipos+1);

901

ipos = name.rfind(

'_'

);

if

(ipos!=string::npos) ipos= name.rfind(

'_'

, ipos-1);

902  if

(ipos!=string::npos) name.erase(0, ipos+1);

904

(problem->type ==

eFrameShift

&& !keep_frameshifted)

910

{ problem_names[name]=

ProblemType

(problem->type); added=

true

; }

912  NcbiCerr

<<

"CollectFrameshiftedSeqs: "

<< feat->first

914

<<

"("

<< name <<

")" 915

<< (added ?

"added"

:

"skipped"

) <<

NcbiEndl

;

918  return

problem_names.

size

();

926  NcbiCerr

<<

"append_misc_feature: FATAL: do not have problems for "

<< name <<

NcbiEndl

;

934

list<CRef<CSeq_id> >& na_id = (*na)->SetSeq().SetId();

937  if

( !(*gen_feature)->GetData().IsFtable() )

continue

;

940

Tproblem_misced problem_misced;

943  if

( !(problem->type & problem_type) )

continue

;

949  if

(from<0)

continue

;

956

strand = problem->strand;

957

message = problem->misc_feat_message;

958  if

(message.size()==0)

continue

;

959  if

(problem_misced.find(problem->type) != problem_misced.end() &&

960

problem_misced[problem->type].find(message) != problem_misced[problem->type].end()

962  else

problem_misced[problem->type][message] =

true

;

964  while

((pos=message.find_first_of(

"\n\r"

))!=string::npos)

971

feat->

SetData

().SetImp().SetKey(

"misc_feature"

);

974

feat->

SetLocation

().SetInt().SetId(**na_id.begin());

976

(*gen_feature)->SetData().SetFtable().push_back(feat);

int CollectFrameshiftedSeqs(map< string, string > &problem_names)

int CollectRNAFeatures(TProblem_locs &problem_locs)

static bool hasProblems(const CBioseq &seq, diagMap &diag, const EProblem type)

static bool PrintDetails(int current_verbosity=m_current_verbosity)

CConstBeginInfo ConstBegin(void)

void erase_problems(const string &qname, diagMap &diag, const EProblem type)

void GetLocMap(LocMap &loc_map, const CSeq_annot::C_Data::TFtable &feats)

int RemoveInterim2(CBioseq::TAnnot &annots)

static void IncreaseVerbosity(void)

void reportProblemMessage(const string &message, ostream &out=NcbiCout)

void reportProblemType(const EProblem type, ostream &out=NcbiCout)

static string ProblemType(const EProblem type)

void reportProblemSequenceName(const string &name, ostream &out=NcbiCout)

int RemoveProblems(map< string, string > &problem_seqs, LocMap &loc_map)

static bool is_prot_entry(const CBioseq &seq)

static void DecreaseVerbosity(void)

static void PopVerbosity(void)

static void getFromTo(const CSeq_loc &loc, TSeqPos &from, TSeqPos &to, ENa_strand &strand)

void reportProblems(const bool report_and_forget, diagMap &diag, ostream &out, const CBioseq::TAnnot &annots, const EProblem type)

void NormalizeSeqentry(CSeq_entry &entry)

void append_misc_feature(CBioseq_set::TSeq_set &seqs, const string &name, EProblem problem_type)

static void PushVerbosity(void)

namespace ncbi::objects::

Template class for iteration on objects of class C (non-medifiable version)

Template class for iteration on objects of class C.

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

std::ofstream out("events_result.xml")

main entry point for tests

#define test(a, b, c, d, e)

static void DLIST_NAME() remove(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define MSerial_AsnText

I/O stream manipulators –.

static string GetStringDescr(const CBioseq &bioseq, EStringFormat fmt)

@ eOverlap

CSeq_locs overlap.

NCBI_NS_STD::string::size_type SIZE_TYPE

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

void SetData(TData &value)

Assign a value to Data data member.

ENa_strand

strand of nucleic acid

TSet & SetSet(void)

Select the variant.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSetAnnot(void) const

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

void ResetAnnot(void)

Reset Annot data member.

bool IsSetSeq_set(void) const

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

bool IsSetDescr(void) const

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

bool IsSet(void) const

Check if variant Set is selected.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

TSeq_set & SetSeq_set(void)

Assign a value to Seq_set data member.

list< CRef< CSeqdesc > > Tdata

bool IsSetAnnot(void) const

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

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

void ResetAnnot(void)

Reset Annot data member.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

bool IsEntrys(void) const

Check if variant Entrys is selected.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

string GetLocationString(const CSeq_feat &f)

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

const GenericPointer< typename T::ValueType > T2 value

int addProblems(list< problemStr > &dest, const list< problemStr > &src)

string diagName(const string &type, const string &value)

string GetStringDescr(const CBioseq &bioseq)

string GetLocusTag(const CSeq_feat &f, const LocMap &loc_map)

string printed_range(const TSeqPos from2, const TSeqPos to2)

static wxAcceleratorEntry entries[3]

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