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

48

FILE *fpt = fopen(

file

,

"r"

);

56

CBioseq::TId::iterator id;

62  id

= seq->

SetId

().begin();

66

<<

"CSeq_id::GetStringDescr for prefix = " 69

<<

"GetStringDescr for prefix = " 79

string::size_type ipos = prefix.rfind(

'|'

);

80  if

(ipos != string::npos) prefix.erase(ipos+1);

89  if

((s=strstr(

str

,

"Query= "

))!=

NULL

)

109

<<

"before applying tagmap = " 114

<<

"after applying tagmap = " 127  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while parsing long protein names"

<<

NcbiEndl

;

130  CRegexp

re_length(

"Length=(\\d+)|\\((\\d+) letters\\)"

);

132  auto

qLenStr = re_length.

GetSub

(

str

,1);

133  if

(qLenStr.empty()) qLenStr = re_length.

GetSub

(

str

,2);

134

qLen = NStr::StringToNumeric<long>(qLenStr);

138

blastMap[qName].qLen = qLen;

139

blastMap[qName].qName = qName;

142

<< qName <<

":"

<< qLen <<

NcbiEndl

;

152

blastMap[qName].hits.resize(ihit+1);

155  if

((s=strstr(

str

,

"gi|"

)) !=

NULL

)

158

sbjGIs.push_back(gi);

165  char

bigbuf[9900]; *bigbuf =

'\0'

;

168  CRegexp

re_length_in_align(

"Length\\s*=\\s*(\\d+)"

);

177  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while parsing hits"

<<

NcbiEndl

;

180  if

((s=strstr(

str

,

"gi|"

)) !=

NULL

)

183

sbjGIs.push_back(gi);

192

blastMap[qName].hits[ihit].sbjGIs = sbjGIs;

195  long

sbjLen = NStr::StringToNumeric<long>(re_length_in_align.

GetSub

(

str

, 1));

196

blastMap[qName].hits[ihit].sbjLen = sbjLen;

202  for

(

int

k=1; k < 2; ++s)

if

(*s ==

' '

) ++k;

210  while

(*s && (*s !=

'\n'

))

214  while

((ipos = sbjName.find_last_of(

"\r\n"

)) != string::npos)

216

sbjName.erase(ipos,1);

220

blastMap[qName].hits[ihit].sbjName = sbjName;

222  if

(*s ==

'\n'

) { ++s; }

227  if

(strstr(s,

"gi|"

)!= s)

229  while

(*s && (*s !=

'\n'

)) {s++; }

232  while

(strstr(

str

,

"Score = "

)==

NULL

)

236  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while skipping to Score line"

<<

NcbiEndl

;

241

s = strstr(

str

,

"Score = "

); s+=strlen(

"Score = "

);

242  double

bitscore = atof(s);

243

blastMap[qName].hits[ihit].bitscore = bitscore;

246  if

(

str

[strlen(

str

)-1] ==

'\n'

)

str

[strlen(

str

)-1] =

' '

;

248

s = strstr(

str

,

"Expect = "

); s+=strlen(

"Expect = "

);

249  double

eval = atof(s);

250

blastMap[qName].hits[ihit].eval = eval;

254  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while reading Identities line"

<<

NcbiEndl

;

257

s = strstr(

str

,

"Identities = "

); s+=strlen(

"Identities = "

);

258  long

nident = atoi(s);

259

blastMap[qName].hits[ihit].nident = nident;

260

s = strstr(s,

"/"

); s++;

261  long

alilen = atoi(s);

262

blastMap[qName].hits[ihit].alilen = alilen;

263

s = strstr(s,

"("

); s++;

264  double

pident = atof(s);

265

blastMap[qName].hits[ihit].pident = pident;

267

s = strstr(

str

,

"Positives = "

); s+=strlen(

"Positives = "

);

269

blastMap[qName].hits[ihit].npos = npos;

270

s = strstr(s,

"/"

); s++;

272

s = strstr(s,

"("

); s++;

274

blastMap[qName].hits[ihit].ppos = ppos;

277  CRegexp

re_query_in_align(

"^Query[: ]"

);

282  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while skipping to Query: line"

<<

NcbiEndl

;

291  char label

[10], seqal[100];

292  long

sbjstart =0 ,sbjend, ret;

295

ret = sscanf(

str

,

"%s%ld%s%ld"

,

label

, &q_start, seqal, &q_end);

296  if

(ret != 4) { printf(

"\nERROR line: %s"

,

str

);

return

0;}

300  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while parsing first alignment line"

<<

NcbiEndl

;

305  CRegexp

re_subj_in_align(

"^Sbjct[: ]"

);

310  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while skipping to Sbjct:line"

<<

NcbiEndl

;

319

ret = sscanf(

str

,

"%s%ld%s%ld"

,

label

, &tmpstart, seqal, &sbjend);

320  if

(ret != 4) { printf(

"\nERROR line: %s"

,

str

);

return

0;}

322  if

(sbjstart == 0) sbjstart = tmpstart;

326  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while appending to alignment I"

<<

NcbiEndl

;

332  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while parsing Query: line"

<<

NcbiEndl

;

339

ret = sscanf(

str

,

"%s%ld%s%ld"

,

label

, &tmpstart, seqal, &q_end);

340  if

(ret != 4) { printf(

"\nERROR line: %s"

,

str

);

return

0;}

343  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while parsing after Query: line"

<<

NcbiEndl

;

349  NcbiCerr

<<

"CReadBlastApp::ReadBlast: ERROR: no next line in ("

<<

file

<<

") while parsing new Sbjt line"

<<

NcbiEndl

;

357

blastMap[qName].hits[ihit].alignment = alignment;

358

blastMap[qName].hits[ihit].sbjstart = sbjstart;

359

blastMap[qName].hits[ihit].sbjend = sbjend ;

360

blastMap[qName].hits[ihit].q_start = q_start;

361

blastMap[qName].hits[ihit].q_end = q_end ;

380  for

(seq=

Begin

(); seq; ++seq)

389  if

(blastMap.

find

(qname) == blastMap.

end

() )

391  NcbiCerr

<<

"WARNING: sequence "

<< qname <<

" does not have blast results, might be a naming convention mismatch"

<<

NcbiEndl

;

401  NcbiCerr

<<

"Removing some hits from previous version of the same genome:"

;

416  for

(

unsigned int

ihit=0; ihit < blastMap[qname].hits.

size

(); ihit++)

418  bool

prev_version=

false

;

420  for

(list<long>::const_iterator mygi = blastMap[qname].hits[ihit].sbjGIs.

begin

();

421

mygi!=blastMap[qname].hits[ihit].sbjGIs.

end

();

429  NcbiCerr

<<

"CReadBlastApp::StoreBlast: blast hit to the protein from previous version: " 440

annotList.push_back(annot);

444

desc->

SetName

(blastMap[qname].hits[ihit].sbjName);

445

annot->

SetDesc

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

449

desc->

SetComment

(blastMap[qname].hits[ihit].alignment);

451

annot->

SetDesc

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

457

alignList.push_back(align);

467

id_vector.push_back(qid);

472

id_vector.push_back(sid);

476

start_vector.push_back(1);

477

start_vector.push_back(1);

481

len_vector.push_back(1);

482

len_vector.push_back(1);

487  bounds

.push_back(qBounds);

489  bounds

.push_back(sbjBounds);

490

qBounds->

SetInt

().SetFrom(blastMap[qname].hits[ihit].q_start);

491

qBounds->

SetInt

().SetTo (blastMap[qname].hits[ihit].q_end);

492

qBounds->

SetInt

().SetId().SetLocal().SetId(1);

493

sbjBounds->

SetInt

().SetFrom(blastMap[qname].hits[ihit].sbjstart);

494

sbjBounds->

SetInt

().SetTo (blastMap[qname].hits[ihit].sbjend);

495

sbjBounds->

SetInt

().SetId().SetLocal().SetId(1);

502

iscore++; scores[iscore]=

new CScore

;

503

scores[iscore]->

SetId

().SetStr(

"sbjLen"

);

504

scores[iscore]->SetValue().SetInt(blastMap[qname].hits[ihit].sbjLen);

505

iscore++; scores[iscore]=

new CScore

;

506

scores[iscore]->

SetId

().SetStr(

"score"

);

507

scores[iscore]->SetValue().SetReal(blastMap[qname].hits[ihit].bitscore);

508

iscore++; scores[iscore]=

new CScore

;

509

scores[iscore]->

SetId

().SetStr(

"e_value"

);

510

scores[iscore]->SetValue().SetReal(blastMap[qname].hits[ihit].eval);

511

iscore++; scores[iscore]=

new CScore

;

512

scores[iscore]->

SetId

().SetStr(

"num_ident"

);

513

scores[iscore]->SetValue().SetInt(blastMap[qname].hits[ihit].nident);

514

iscore++; scores[iscore]=

new CScore

;

515

scores[iscore]->

SetId

().SetStr(

"alilen"

);

516

scores[iscore]->SetValue().SetInt(blastMap[qname].hits[ihit].alilen);

517

iscore++; scores[iscore]=

new CScore

;

518

scores[iscore]->

SetId

().SetStr(

"per_ident"

);

519

scores[iscore]->SetValue().SetReal(blastMap[qname].hits[ihit].pident);

520

iscore++; scores[iscore]=

new CScore

;

521

scores[iscore]->

SetId

().SetStr(

"num_sim"

);

522

scores[iscore]->SetValue().SetInt(blastMap[qname].hits[ihit].npos);

523

iscore++; scores[iscore]=

new CScore

;

524

scores[iscore]->

SetId

().SetStr(

"per_sim"

);

525

scores[iscore]->SetValue().SetReal(blastMap[qname].hits[ihit].ppos);

526

scores.resize(scores.size()+blastMap[qname].hits[ihit].sbjGIs.

size

());

528  for

(list<long>::const_iterator gii=blastMap[qname].hits[ihit].sbjGIs.

begin

();

529

gii!=blastMap[qname].hits[ihit].sbjGIs.

end

(); ++gii)

531

iscore++; scores[iscore]=

new CScore

;

532

scores[iscore]->

SetId

().SetStr(

"use_this_gi"

);

533

scores[iscore]->SetValue().SetInt(*gii);

551  for

(seq=

Begin

(); seq; ++seq)

558  if

(blastMap.

find

(qname) == blastMap.

end

() )

continue

;

562  int

numQcoversHits=0;

563  int

numScoversHits=0;

566  const blastStr

& thisStr=blastMap.

find

(qname)->second;

568  int

qLen = blastMap[qname].qLen;

569

vector<problemStr> problems;

570  for

(

unsigned int

ihit=0; ihit < thisStr.

hits

.size(); ihit++)

572  const hitStr

& thisHitStr = thisStr.

hits

[ihit];

573  int

q_ali_len = thisHitStr.

q_end

- thisHitStr.

q_start

+1;

575  int

sLen = thisHitStr.

sbjLen

;

576  string

sname = thisHitStr.

sbjName

;

577  if

(sname.find(

" PRK"

)!=string::npos)

continue

;

578  if

(sname.find(

" CHL"

)!=string::npos)

continue

;

579  if

(sname.find(

" MTH"

)!=string::npos)

continue

;

580  if

(sname.find(

" MTF"

)!=string::npos)

continue

;

581  if

(sname.find(

" PHA"

)!=string::npos)

continue

;

582  if

(sname.find(

" PTZ"

)!=string::npos)

continue

;

594  char

bufferchar[2048]; memset(bufferchar, 0, 2048);

595

strstream

buffer

(bufferchar, 2048);

602  buffer

<<

"Subject"

<<

"\t" 607  string

debug_test =

buffer

.str();

613

problems.push_back(problem);

623  if

(numScoversHits && !numQcoversHits)

625  ITERATE

(vector<problemStr>, problem, problems)

627  m_diag

[qname].problems.push_back(*problem);

629  char

bufferchar[2048]; memset(bufferchar, 0, 2048);

630

strstream

buffer

(bufferchar, 2048);

632  NcbiCerr

<< qname <<

"("

<< qLen <<

")" 633

<<

" is a potential partial annotation."

<<

NcbiEndl

;

635

<< numHits <<

" hits to CDD db, " 636

<< numScoversHits <<

" cover the query and in only " 637

<< numQcoversHits <<

" cases query covers the subject" 640  m_diag

[qname].problems.push_back(problem1);

static bool PrintDetails(int current_verbosity=m_current_verbosity)

map< string, string > m_tagmap

static void IncreaseVerbosity(void)

static char * next_w(char *w)

list< long > m_previous_genome

int ProcessCDD(map< string, blastStr > &blastMap)

static int skip_toprot(CTypeIterator< CBioseq > &seq)

int ReadBlast(const char *file, map< string, blastStr > &blastMap)

static double m_entireThreshold

int StoreBlast(map< string, blastStr > &blastMap)

static char * skip_space(char *w)

static void DecreaseVerbosity(void)

static double m_partThreshold

static double m_eThreshold

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

static const char * bounds[]

static const char * str(char *buf, int n)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

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

bool IsMatch(CTempString str, TMatch flags=fMatch_default)

Check existence substring which match a specified pattern.

CTempString GetSub(CTempString str, size_t idx=0) const

Get pattern/subpattern from previous GetMatch().

static const char label[]

TId & SetId(void)

Select the variant.

TScore & SetScore(void)

Assign a value to Score data member.

vector< CRef< CScore > > TScore

void SetSegs(TSegs &value)

Assign a value to Segs data member.

vector< TSignedSeqPos > TStarts

void SetType(TType value)

Assign a value to Type data member.

vector< CRef< CSeq_id > > TIds

list< CRef< CSeq_loc > > TBounds

void SetId(TId &value)

Assign a value to Id data member.

TBounds & SetBounds(void)

Assign a value to Bounds data member.

@ eType_partial

mapping pieces together

TLocal & SetLocal(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

TId & SetId(void)

Assign a value to Id data member.

void SetDesc(TDesc &value)

Assign a value to Desc data member.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

TName & SetName(void)

Select the variant.

list< CRef< CSeq_align > > TAlign

TComment & SetComment(void)

Select the variant.

list< CRef< CSeq_annot > > TAnnot

Miscellaneous common-use basic types and functionality.

string GetStringDescr(const CBioseq &bioseq)

C++ wrappers for the Perl-compatible regular expression (PCRE) library.

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