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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/id1__fetch_8cpp_source.html below:

NCBI C++ ToolKit: src/app/id1_fetch/id1_fetch.cpp Source File

96 virtual void Init

(

void

);

97 virtual int Run

(

void

);

98 virtual void Exit

(

void

);

129

arg_desc->AddOptionalKey

130

(

"gi"

"SeqEntryID"

131 "GI id of the Seq-Entry to fetch"

133

arg_desc->SetConstraint

137

arg_desc->AddDefaultKey

138

(

"fmt"

"OutputFormat"

139 "Format to dump the resulting data in"

141

arg_desc->SetConstraint

143 "asn"

"asnb"

"xml"

"genbank"

"genpept"

"fasta"

144 "quality"

"docsum"

));

147

arg_desc->AddDefaultKey

148

(

"out"

"ResultFile"

149 "File to dump the resulting data to"

153

arg_desc->AddOptionalKey

154

(

"log"

"LogFile"

155 "File to post errors and messages to"

160

arg_desc->AddOptionalKey

161

(

"db"

"Database"

166

arg_desc->AddOptionalKey

167

(

"ent"

"EntityNumber"

168 "(Sub)entity number (retrieval number) to dump"

170

arg_desc->SetConstraint

174

arg_desc->AddDefaultKey

175

(

"lt"

"LookupType"

178

arg_desc->SetConstraint

180 "entry"

"state"

"ids"

"history"

"revisions"

"none"

));

183

arg_desc->AddOptionalKey

184

(

"in"

"RequestFile"

185 "File with list of GIs, (versioned) accessions, FASTA SeqIDs to dump"

189

arg_desc->AddOptionalKey

190

(

"maxplex"

"MaxComplexity"

191 "Maximum complexity to return"

193

arg_desc->SetConstraint

195 "entry"

"bioseq"

"bioseq-set"

"nuc-prot"

199

arg_desc->AddOptionalKey

200

(

"extfeat"

"ExtFeat"

201 "Add features, delimited by ',': " 202 "SNP, SNP_graph, CDD, MGC, HPRD, STS, tRNA, Exon"

206

arg_desc->AddOptionalKey

207

(

"flat"

"FlatID"

208 "Flattened SeqID; format can be\n" 209 "\t'type([name][,[accession][,[release][,version]]])'" 210 " [e.g., '5(HUMHBB)'],\n" 211 "\ttype=accession[.version], or type:number"

215

arg_desc->AddOptionalKey

216

(

"fasta"

"FastaID"

225

arg_desc->AddOptionalKey

226

(

"query"

"EntrezQueryString"

227 "Generate GI list by Entrez query given on command line"

229

arg_desc->AddOptionalKey

230

(

"qf"

"EntrezQueryFile"

231 "Generate GI list by Entrez query in given file"

235 string

prog_description =

236 "Fetch SeqEntry from ID server by its GI ID, possibly obtained from\n" 237 "its SeqID or an Entrez query"

;

238

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

239

prog_description,

false

);

242

arg_desc->AddDefaultKey

243

(

"repeat"

244 "Repeat fetch number of times"

248

arg_desc->AddOptionalKey

249

(

"timeout"

"Timeout"

250 "Network connection timeout in seconds"

263 return iscntrl

((

unsigned char

) c) ?

true

false

;

273 if

( args[

"log"

] ) {

285 if

( args[

"timeout"

] ) {

286 int

timeout = args[

"timeout"

].AsInteger();

296 const string

& fmt = args[

"fmt"

].AsString();

298 if

(args[

"gi"

]) id_count++;

299 if

(args[

"in"

]) id_count++;

300 if

(args[

"flat"

]) id_count++;

301 if

(args[

"fasta"

]) id_count++;

302 if

(args[

"query"

]) id_count++;

303 if

(args[

"qf"

]) id_count++;

307 "You must supply exactly one argument" 308 " indicating what to look up."

);

310 if

((args[

"query"

] || args[

"qf"

] || fmt ==

"docsum"

)

312 ERR_POST

(

"No Entrez database supplied. Try -db Nucleotide or " 316 if

((fmt ==

"genbank"

|| fmt ==

"genpept"

|| fmt ==

"quality"

)

317

&& args[

"lt"

].AsString() !=

"entry"

) {

318 ERR_POST

(

"The output format '"

<< fmt

319

"' is only available for Seq-Entries."

);

335 int

repeat = args[

"repeat"

].AsInteger();

336 for

(

int

pass = 0; pass < repeat; ++pass ) {

342 if

(args[

"fasta"

]) {

349 if

(args[

"flat"

]) {

358 while

(is && !is.eof()) {

363 if

(

id

empty

()) {

366 if

(

id

.find(

'|'

) !=

NPOS

) {

368

}

else if

(

id

.find_first_of(

":=("

) !=

NPOS

) {

380 if

(args[

"query"

] || args[

"qf"

]) {

385 if

(args[

"query"

]) {

386

e2_element->SetStr(args[

"query"

].AsString());

399 query

.SetExp().push_back(e2_element);

403 if

( !reply->GetCount() ) {

404 ERR_POST

(

"Entrez query returned no results."

);

410

= reply->GetUids().GetConstUidIterator();

425 const string

& fmt = args[

"fmt"

].AsString();

426 const string

= args[

"lt"

].AsString();

428 bool

use_objmgr =

false

;

430 if

(

"none"

) {

433

}

else if

(fmt ==

"docsum"

) {

445 if

( !docs->GetCount() ) {

446 ERR_POST

(

"Entrez query returned no results."

);

450 string

caption, title;

454 if

(it->GetField_name() ==

"Caption"

) {

455

caption = it->GetField_value();

456

}

else if

(it->GetField_name() ==

"Title"

) {

457

title = it->GetField_value();

460

*m_OutputFile << '>

'; 461 if ( !caption.empty() ) { 462 *m_OutputFile << caption; 464 *m_OutputFile << ' '; 465 if ( !title.empty() ) { 466 *m_OutputFile << title; 468 } else if (lt == "entry") { 469 if ( args["maxplex"] || args["extfeat"] ) { 470 CRef<CID1server_back> id1_reply(new CID1server_back); 471 CRef<CID1server_maxcomplex> maxcomplex(new CID1server_maxcomplex); 472 int mp = eEntry_complexities_entry; 473 if ( args["maxplex"] ) { 474 string maxplex = args["maxplex"].AsString(); 475 if ( maxplex == "bioseq" ) { 476 mp = eEntry_complexities_bioseq; 478 else if ( maxplex == "bioseq-set" ) { 479 mp = eEntry_complexities_bioseq_set; 481 else if ( maxplex == "nuc-prot" ) { 482 mp = eEntry_complexities_nuc_prot; 484 else if ( maxplex == "pub-set" ) { 485 mp = eEntry_complexities_pub_set; 488 if ( args["extfeat"] ) { 490 vector<string> extfeat; 491 NStr::Split(args["extfeat"].AsString(), ",", extfeat); 492 ITERATE ( vector<string>, it, extfeat ) { 493 if ( *it == "SNP" ) { 496 else if ( *it == "SNP_graph" ) { 499 else if ( *it == "CDD" ) { 502 else if ( *it == "MGC" ) { 505 else if ( *it == "HPRD" ) { 508 else if ( *it == "STS" ) { 511 else if ( *it == "tRNA" ) { 514 else if ( *it == "Exon" ) { 518 ERR_POST("Unknown extfeat type: "<<*it); 523 maxcomplex->SetMaxplex(mp); 524 maxcomplex->SetGi(gi); 525 reply_object = m_ID1Client.AskGetsefromgi(*maxcomplex, id1_reply); 530 } else if (lt == "state") { 531 CRef<CID1server_back> id1_reply(new CID1server_back); 532 int state = m_ID1Client.AskGetgistate(gi, id1_reply); 533 if (fmt == "fasta") { 534 *m_OutputFile << "gi = " << gi << ", states: "; 535 switch (state & 0xff) { 536 case 0: *m_OutputFile << "NONEXISTENT"; break; // was "NOT EXIST" 537 case 10: *m_OutputFile << "DELETED"; break; 538 case 20: *m_OutputFile << "REPLACED"; break; 539 case 40: *m_OutputFile << "LIVE"; break; 540 default: *m_OutputFile << "UNKNOWN"; break; 543 *m_OutputFile << "|SUPPRESSED"; 546 *m_OutputFile << "|WITHDRAWN"; 549 *m_OutputFile << "|CONFIDENTIAL"; 552 reply_object = id1_reply; 554 } else if (lt == "ids") { 556 CRef<CID1server_back> id1_reply(new CID1server_back); 557 CID1server_back::TIds ids 558 = m_ID1Client.AskGetseqidsfromgi(gi, id1_reply); 559 if (fmt == "fasta") { 562 reply_object = id1_reply; 567 } else if (lt == "history" || lt == "revisions") { 568 CRef<CID1server_back> id1_reply(new CID1server_back); 569 // ignore result -- it'

s simpler to use id1_reply

570 if

(

"history"

) {

575 if

(fmt ==

"fasta"

) {

578

reply_object = id1_reply;

590 ERR_FATAL

(

"Bioseq not found: "

id

.DumpAsFasta());

595

((fmt ==

"fasta"

&& (

"ids"

"entry"

)) ||

598

fmt ==

"genpept"

) ) {

607 ERR_FATAL

(

"Bioseq not found: "

id

.DumpAsFasta());

615

}

else if

(fmt ==

"asnb"

) {

617

}

else if

(fmt ==

"xml"

) {

619

}

else if

(fmt ==

"fasta"

"ids"

) {

623

}

else if

(fmt ==

"fasta"

"entry"

) {

628

}

else if

(fmt ==

"quality"

) {

630

}

else if

(fmt ==

"genbank"

|| fmt ==

"genpept"

) {

631 bool

gp = fmt ==

"genpept"

;

651

unique_ptr<CObjectOStream> asn_output

657 if

(fmt !=

"asnb"

) {

699 SIZE_TYPE

pos = s.find_first_of(

":=("

);

703 string data

= s.substr(pos + 1);

716

vector<string> pieces;

734 if

(it != ids.begin()) {

753 string Get

(

unsigned int

index)

const

{

769

gis.

Add

(

"GI"

Add

(

"--"

);

770

dates.

Add

(

"Loaded"

Add

(

"------"

);

771

dbs.

Add

(

"DB"

Add

(

"--"

);

772

numbers.

Add

(

"Retrieval No."

Add

(

"-------------"

);

778 if

( it->GetDate().IsStr() ) {

779

dates.

Add

(it->GetDate().GetStr());

783

oss << setfill(

'0'

) << setw(2) << date.

GetMonth

() <<

'/' 789 if

( (*it2)->IsGi() ) {

790

gi = (*it2)->GetGi();

791

}

else if

( (*it2)->IsGeneral() ) {

792 dbname

= (*it2)->GetGeneral().GetDb();

794 if

(

tag

.IsStr() ) {

807 for

(

unsigned int n

= 0;

< gis.

Height

();

++) {

825

->GetSeqIdString(

true

);

828 string

title = it->GetTitle();

829 if

(title.find(

"uality"

) ==

NPOS

) {

834

*m_OutputFile << '>

' << id << ' ' << title 835 << " (Length: " << it->GetNumval() 836 << ", Min: " << data.GetMin() 837 << ", Max: " << data.GetMax() << '

)

' << NcbiEndl; 838 for (SIZE_TYPE n = 0; n < data.GetValues().size(); ++n) { 839 *m_OutputFile << setw(3) << static_cast<int>(data.GetValues()[n]); 841 *m_OutputFile << NcbiEndl; 857

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

859

return CId1FetchApp().AppMain(argc, argv);

User-defined methods of the data storage class.

void GetDate(string *label, const string &format) const

Append a custom string representation of the date to the label.

CEntrez2_boolean_element â.

CEntrez2_boolean_exp â.

CEntrez2_eval_boolean â.

TUidIterator GetUidIterator()

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

void SetFormatGenbank(void)

CFlatFileConfig & SetHideSNPFeatures(bool val=true)

void SetMode(const TMode &mode)

CFlatFileConfig & SetShowContigFeatures(bool val=true)

CFlatFileConfig & SetShowContigSources(bool val=true)

void Generate(const CSeq_entry_Handle &entry, CFlatItemOStream &item_os, const multiout &={})

SAnnotSelector & SetAnnotSelector(void)

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

void SetAllowDeadEntries(bool ok)

@ID1server_back.hpp User-defined methods of the data storage class.

void WriteHistoryTable(const CID1server_back &id1_reply)

void WriteQualityScores(CBioseq_Handle &handle)

TGi LookUpFlatSeqID(const string &s)

CEntrez2Client m_E2Client

virtual int Run(void)

Run the application.

CRef< CObjectManager > m_ObjMgr

TGi LookUpRawSeqID(const string &s)

virtual void Init(void)

Initialize the application.

TGi LookUpFastaSeqID(const string &s)

CNcbiOstream * m_OutputFile

void WriteFastaIDs(const list< CRef< CSeq_id > > &ids)

virtual void Exit(void)

Cleanup on application exit.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

string Get(unsigned int index) const

CTextColumn & Add(string s)

vector< string > m_Strings

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

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

main entry point for tests

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

#define GI_FROM(T, value)

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

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.

@ fBinary

Open as binary file; for eInputFile, eOutputFile, eIOFile.

@ fPreOpen

Open file right away; for eInputFile, eOutputFile, eIOFile.

@ eInputFile

Name of file (must exist and be readable)

@ eIntId

Convertible to TIntId (int or Int8 depending on NCBI_INT8_GI)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

#define ERR_FATAL(message)

Posting fatal error and abort.

void SetDiagPostFlag(EDiagPostFlag flag)

Set the specified flag (globally).

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDPF_All

All flags (except for the "unusual" ones!)

@ eDiag_Info

Informational message.

#define NCBI_THROW(exception_class, err_code, message)

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

#define THROW_TRACE_ARGS(exception_class,...)

Throw trace.

virtual const CTypeInfo * GetThisTypeInfo(void) const =0

EIO_Status SetTimeout(const STimeout *timeout, EIO_Event direction=eIO_ReadWrite)

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static int Score(const CRef< CSeq_id > &id)

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

@ fParse_NoFASTA

Don't bother checking for a tag.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

@ fInstantiateGaps

honor specifed gap mode; on by default

@ fAssembleParts

assemble FAR delta sequences; on by dflt

CBioseq_Handle GetBioseqHandleFromTSE(const CSeq_id &id, const CTSE_Handle &tse)

Get bioseq handle for sequence withing one TSE.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void ResetDataAndHistory(void)

Clear all information in the scope except added data loaders.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

SAnnotSelector & ExcludeNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to exclude.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty â pointing to an object and has a non-null value.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

size_t NcbiStreamToString(string *s, CNcbiIstream &is, size_t pos=0)

Input the entire contents of an istream into a string (NULL causes drain).

NCBI_NS_STD::string::size_type SIZE_TYPE

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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

Convert int 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.

unsigned int usec

microseconds (modulo 1,000,000)

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

void SetTool(const TTool &value)

Assign a value to Tool data member.

virtual TRequest & SetDefaultRequest(void)

void SetReturn_UIDs(TReturn_UIDs value)

Assign a value to Return_UIDs data member.

virtual CRef< CEntrez2_boolean_reply > AskEval_boolean(const CEntrez2_eval_boolean &req, TReply *reply=0)

void SetDb(const TDb &value)

Assign a value to Db data member.

void SetQuery(TQuery &value)

Assign a value to Query data member.

virtual CRef< CEntrez2_docsum_list > AskGet_docsum(const CEntrez2_id_list &req, TReply *reply=0)

TYear GetYear(void) const

Get the Year member data.

TMonth GetMonth(void) const

Get the Month member data.

TDay GetDay(void) const

Get the Day member data.

virtual NCBI_NS_NCBI::TGi AskGetgi(const CSeq_id &req, TReply *reply=0)

virtual list< CRef< CID1Seq_hist > > AskGetgihist(const NCBI_NS_NCBI::TGi &req, TReply *reply=0)

virtual list< CRef< CID1Seq_hist > > AskGetgirev(const NCBI_NS_NCBI::TGi &req, TReply *reply=0)

TGi & SetGi(void)

Select the variant.

E_Choice

Choice variants.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TIds

char * dbname(DBPROCESS *dbproc)

Get name of current database.

USING_SCOPE(NCBI_NS_NCBI::objects)

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

constexpr bool empty(list< Ts... >) noexcept

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Process information in the NCBI Registry, including working with configuration files.

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