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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/agpconvert_8cpp_source.html below:

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

100 struct

SSimpleSubsourceInfo {

101 const char

* m_pchSynopsis;

102 const char

* m_pchUsage;

106 static const

TSimpleSubsource sc_SimpleSubsource[] = {

128 virtual void Init

(

void

);

129 virtual int Run

(

void

);

130 virtual void Exit

(

void

);

152 const string

& sTemplateLocation,

181

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

182 "AGP file converter program"

);

186

arg_desc->SetCurrentGroup(

"INPUT"

);

188

arg_desc->AddKey(

"template"

"LOCATION"

189 "The filename of a template Seq-entry or Seq-submit or Bioseq in " 190 "either ASN.1 text or ASN.1 binary or XML (autodetected). A series of Seqdescs " 191 "may optionally follow the main ASN.1 object." 192 "Alternatively, if the LOCATION looks reasonably like a GenBank identifier and " 193 "doesn't exist as a file, the template is loaded from genbank instead."

195

arg_desc->AddFlag(

"keeptemplateannots"

196 "Unless this flag is set, the annots from the template are removed"

);

199

(1, 32766,

"AGP files to process"

202

arg_desc->SetCurrentGroup(

"OUTPUT"

);

204

arg_desc->AddOptionalKey(

"outdir"

"output_directory"

205 "Directory for output files " 206 "(defaults to current directory)"

208

arg_desc->AddOptionalKey(

"ofs"

209 "Output filename suffix " 210 "(default is \".ent\" for Seq-entry " 211 "or \".sqn\" for Seq-submit"

213

arg_desc->AddFlag(

"stdout"

"Write to stdout rather than files. This does not work for Seq-submits. " 214 "Implies -no_asnval."

);

215

arg_desc->AddDefaultKey(

216 "output-type"

"ASN_OBJECT_TYPE"

217 "This lets you force what kind of object is used for output. " 218 " Forcing may cause some data to be thrown out (Example: " 219 "if input is a Seq-submit and you force the output to be a " 220 "Seq-entry, then the Seq-submit's data will be disregarded)"

223

arg_desc->SetConstraint(

"output-type"

225 "AUTO"

"Seq-entry"

));

228

arg_desc->SetCurrentGroup(

"VALIDATION"

);

230

arg_desc->AddOptionalKey(

"components"

"components_file"

231 "Bioseq-set of components, used for " 234

arg_desc->AddFlag(

"no_asnval"

235 "Do not validate using asnval"

);

237

arg_desc->SetCurrentGroup(

"DESCRIPTORS"

);

239

arg_desc->AddOptionalKey(

"dl"

"definition_line"

240 "Definition line (title descriptor)"

243

arg_desc->AddOptionalKey(

"nt"

"tax_id"

244 "NCBI Taxonomy Database ID"

247

arg_desc->AddOptionalKey(

"on"

"org_name"

251

arg_desc->AddOptionalKey(

"sn"

"strain_name"

257 ITERATE

( TSimpleSubsourceMap, simple_src_it, sc_SimpleSubsourceMap ) {

258 const string

& sArgName = simple_src_it->first;

259 const

SSimpleSubsourceInfo &

info

= simple_src_it->second;

260

arg_desc->AddOptionalKey(sArgName,

info

.m_pchSynopsis,

266

arg_desc->SetCurrentGroup(

"SEQ-IDS"

);

268

arg_desc->AddFlag(

"fasta_id"

"Parse object ids (col. 1) " 269 "as fasta-style ids if they contain '|'"

);

270

arg_desc->AddDefaultKey(

"general_id"

"general_db"

271 "if set to non-empty string, local ids for object seq-ids will " 272 "become general ids belonging to the given database"

275

arg_desc->SetCurrentGroup(

"OTHER"

);

277

arg_desc->AddFlag(

"fuzz100"

"For gaps of length 100, " 278 "put an Int-fuzz = unk in the literal"

);

280

arg_desc->AddOptionalKey(

"chromosomes"

"chromosome_name_file"

281 "Mapping of col. 1 names to chromsome " 282 "names, for use as SubSource"

284

arg_desc->AddFlag(

"gap-info"

285 "Set Seq-gap (gap type and linkage) in delta sequence"

);

286

arg_desc->AddFlag(

"len-check"

287 "Die if AGP's length does not match the length of the original template."

);

298 if

((*db_tag)->GetDb() ==

"taxon"

) {

305 "expected exactly one"

);

334

args[

"template"

].AsString(),

339 if

( ! args[

"keeptemplateannots"

] ) {

345 const string

& dl = args[

"dl"

].AsString();

348 if

((*desc)->IsTitle()) {

349 throw

runtime_error(

"-dl given but template contains a title"

);

356 if

(args[

"nt"

] || args[

"on"

] || args[

"sn"

] ||

362 if

((*desc)->IsSource()) {

363 throw

runtime_error(

"BioSource specified on command line but " 364 "template contains BioSource"

);

372 ITERATE

( TSimpleSubsourceMap, simple_src_it, sc_SimpleSubsourceMap ) {

373 const string

& sArgName = simple_src_it->first;

374 const

SSimpleSubsourceInfo &

info

= simple_src_it->second;

375 if

( args[sArgName] ) {

378

sub_source->

SetName

(args[sArgName].AsString());

390 if

( args[

"fuzz100"

] ) {

393 if

( args[

"fasta_id"

] ) {

396 if

( args[

"gap-info"

] ) {

399 if

( args[

"len-check"

] ) {

405

fAgpConvertOutputFlags,

409 const string

& sGeneralIdDb = args[

"general_id"

].AsString();

410 if

( ! sGeneralIdDb.empty() ) {

411 class

CLocalToGeneralIdTransformer :

415

CLocalToGeneralIdTransformer(

const string

& sGeneralDb)

416

: m_sGeneralDb(sGeneralDb) { }

420 if

( ! pSeqId || ! pSeqId->IsLocal() ) {

426

dbtag.

SetDb

(m_sGeneralDb);

427 if

( pSeqId->GetLocal().IsId() ) {

428

dbtag.

SetTag

().SetId( pSeqId->GetLocal().GetId() );

429

}

else if

( pSeqId->GetLocal().IsStr() ) {

430

dbtag.

SetTag

().SetStr( pSeqId->GetLocal().GetStr() );

435

pSeqId->Assign( *pNewSeqId );

443 new

CLocalToGeneralIdTransformer(sGeneralIdDb) );

451 if

(args[

"components"

]) {

459 if

(args[

"chromosomes"

]) {

464

vector<string> vecAgpFileNames;

465 for

(

size_t

idx = 1; idx <= args.

GetNExtra

(); ++idx ) {

466

vecAgpFileNames.push_back( args[idx].AsString() );

467 if

( !

CFile

(vecAgpFileNames.back()).

Exists

() ) {

468 throw

runtime_error(

"AGP file not found: "

+ vecAgpFileNames.back() );

472 if

( args[

"stdout"

] ) {

476 if

( args[

"output-type"

].AsString() ==

"Seq-entry"

) {

482

fOutputBioseqsFlags );

484 if

( ! args[

"outdir"

] ) {

485 throw

runtime_error(

"Please specify -stdout or -outdir"

);

490

args[

"outdir"

].AsString(),

492

( args[

"ofs"

] ? args[

"ofs"

].AsString() :

kEmptyStr

493

( args[

"no_asnval"

] ?

NULL

: &asnval_runner ) );

507 const char

* pchCommand =

"asnval"

;

508 const char

* asnval_argv[] = {

512 "-i"

file

.c_str(),

518 for

(

size_t

idx = 0; asnval_argv[idx]; ++idx ) {

532 const string

& sTemplateLocation,

543 if

( !

CDirEntry

(sTemplateLocation).IsFile() ) {

545 if

( !

CRegexpUtil

(sTemplateLocation).Exists(

"^[A-Za-z0-9_|]+(\\.[0-9]+)?$"

) ) {

546 throw

runtime_error(

"This is not a valid sequence identifier: "

+ sTemplateLocation);

558 throw

runtime_error(

"Invalid sequence identifier: "

+ sTemplateLocation);

587 "template file seems to be in an unsupported format: " 595

unique_ptr<CObjectIStream> pObjIstrm(

599 const string

sType = pObjIstrm->ReadFileHeader();

602 if

( sType == CSeq_entry::GetTypeInfo()->GetName() ) {

605

}

else if

( sType == CBioseq::GetTypeInfo()->GetName() ) {

609

out_ent_templ->

SetSeq

( *pBioseq );

610

}

else if

( sType == CSeq_submit::GetTypeInfo()->GetName() ) {

611

pObjIstrm->Read(

ObjectInfo

(*out_submit_templ),

616 throw

runtime_error(

"Seq-submit template must contain " 617 "exactly one Seq-entry"

);

619

}

else if

( sType == CSubmit_block::GetTypeInfo()->GetName() ) {

627

out_submit_templ->

SetSub

(*submit_block);

633

out_submit_templ->

SetData

().SetEntrys().push_back(ent);

636 "Submit-block. Object seems to be of type: "

<< sType);

640 if

( out_submit_templ->

IsEntrys

() ) {

641

out_ent_templ = out_submit_templ->

SetData

().SetEntrys().front();

646 if

(out_ent_templ->

IsSet

()) {

647 unsigned int

num_nuc_ents = 0;

651 if

((*ent_iter)->GetSeq().GetInst().IsNa()) {

653 tmp

->Assign(**ent_iter);

658

desc->

Assign

(**desc_iter);

659 tmp

->SetSeq().SetDescr().Set().push_back(desc);

663 if

(num_nuc_ents == 1) {

666 throw

runtime_error(

"template contains " 668

" nuc. Seq-entrys; should contain 1"

);

683 if

( out_submit_templ->

IsEntrys

() ) {

692 if

( ! out_ent_templ->

IsSeq

() ) {

693 throw

runtime_error(

"The Seq-entry must be a Bioseq not a Bioseq-set."

);

696 if

( args[

"output-type"

].AsString() ==

"Seq-entry"

) {

709 ITERATE

( TSimpleSubsourceMap, simple_src_it, sc_SimpleSubsourceMap ) {

710 const string

& sArgName = simple_src_it->first;

711 if

( args[sArgName] ) {

728 if

( ! args[

"on"

] && ! args[

"nt"

] ) {

734 throw

runtime_error(

"failure contacting taxonomy server"

);

742 const string

& inp_taxname = args[

"on"

].AsString();

754 throw

runtime_error(

"taxonomy server lookup failed"

);

756 if

(!on_result->GetIs_species_level()) {

757 throw

runtime_error(

"supplied name is not species-level"

);

759 if

(inp_orgref->

GetTaxname

() != inp_taxname) {

760

cerr <<

"** Warning: taxname returned by server (" 761

<< on_result->GetOrg().GetTaxname()

762

") differs from that supplied with -on (" 763

<< inp_taxname <<

")"

<< endl;

774 const string

& inp_strain_name = args[

"sn"

].AsString();

775

vector<string> strain_names;

780

strain_names.push_back((*mod)->GetSubname());

783 if

(!(strain_names.size() == 1

784

&& strain_names[0] == inp_strain_name))

786

cerr <<

"** Warning: strain name "

<< inp_strain_name

787

" provided but server lookup yielded "

;

788 if

(strain_names.empty()) {

789

cerr <<

"no strain name"

<< endl;

791

cerr <<

NStr::Join

(strain_names,

" and "

) << endl;

799

nt_result = cl.

GetById

(inp_taxid);

802

" is not species-level"

);

804

nt_result->

SetOrg

().ResetSyn();

806 if

(db_taxid != inp_taxid) {

807

cerr <<

"** Warning: taxid returned by server (" 809

") differs from that supplied with -nt (" 810

<< inp_taxid <<

")"

<< endl;

814 if

(on_taxid != db_taxid) {

815 throw

runtime_error(

"taxid from name lookup (" 817

") differs from that from " 863

cerr << sMessage << endl;

885 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

static TTaxId s_GetTaxid(const COrg_ref &org_ref)

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

void remove_if(Container &c, Predicate *__pred)

Subclass this to override how errors are handled (example: to stop early on some kinds of errors)

This gets called after each file is written, so the caller can do useful things like run asnval on ev...

void OutputBioseqs(CNcbiOstream &ostrm, const std::vector< std::string > &vecAgpFileNames, TOutputBioseqsFlags fFlags=0, size_t uMaxBioseqsToWrite=std::numeric_limits< size_t >::max()) const

Outputs the result from the AGP file names as ASN.1.

@ fOutputBioseqsFlags_WrapInSeqEntry

Bioseqs and Bioseq-sets should always be wrapped in a Seq-entry.

@ fOutputBioseqsFlags_DoNOTUnwrapSingularBioseqSets

Specify this if Bioseq-sets with just one Bioseq in them should _NOT_ be unwrapped into a Bioseq.

EError

The different kinds of errors that could occur while processing.

@ eError_SuggestUsingFastaIdOption

@ eError_WrongNumberOfSourceDescs

@ eError_ComponentTooShort

@ eError_SubmitBlockIgnoredWhenOneBigBioseqSet

@ eError_EntrySkippedDueToFailedComponentValidation

@ eError_ChromosomeFileBadFormat

@ eError_OutputDirNotFoundOrNotADir

@ eError_ChromosomeIsInconsistent

@ eError_ChromosomeMapIgnoredBecauseChromosomeSubsourceAlreadyInTemplate

@ eError_ComponentNotFound

@ eError_AGPLengthMismatchWithTemplateLength

void SetComponentsBioseqSet(CConstRef< objects::CBioseq_set > pComponentsBioseqSet)

Give a bioseq-set containing all the components pieces, for verification.

void OutputOneFileForEach(const string &sDirName, const std::vector< std::string > &vecAgpFileNames, const string &sSuffix=kEmptyStr, IFileWrittenCallback *pFileWrittenCallback=nullptr) const

Outputs the results of each Seq-entry (or Seq-submit if Submit-block was given) into its own file in ...

void LoadChromosomeMap(CNcbiIstream &chromosomes_istr)

Input has 2 tab-delimited columns: id, then chromosome name.

@ fOutputFlags_Fuzz100

For gaps of length 100, put an Int-fuzz = unk in the literal.

@ fOutputFlags_FastaId

Parse object ids (col. 1) as fasta-style ids if they contain '|'.

@ fOutputFlags_SetGapInfo

Set Seq-gap (gap type and linkage) in delta sequence.

@ fOutputFlags_AGPLenMustMatchOrig

When set, we give an error on AGP objects that don't have the same length as the original template.

int TOutputFlags

Bitwise-OR of EOutputFlags.

void SetIdTransformer(IIdTransformer *pIdTransformer)

When this reads an id, it will use the supplied transformer (if any) to change the CSeq_id.

virtual void Notify(const string &file)

virtual void HandleError(CAgpConverter::EError eError, const string &sMessage) const

Default is to print to cerr, but feel free to override in a subclass.

virtual void Init(void)

Initialize the application.

void x_HandleTaxArgs(CRef< CSeqdesc > source_desc)

virtual void Exit(void)

Cleanup on application exit.

CRef< CCustomErrorHandler > m_pCustomErrorHandler

CAgpconvertApplication(void)

bool x_IsAnySimpleSubsourceArgSet(void)

virtual int Run(void)

Run the application.

void x_LoadTemplate(const string &sTemplateLocation, CRef< CSeq_entry > &out_ent_templ, CRef< CSeq_submit > &out_submit_templ)

EFormat

The formats are checked in the same order as declared here.

@ eBinaryASN

Binary ASN.1.

static const char * GetFormatName(EFormat format)

static EFormat Format(const string &path, EOnError onerror=eDefault)

Guess file format.

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

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

bool IsEntrys(void) const

class CStaticArrayMap<> is an array adaptor that provides an STLish interface to statically-defined a...

CRef< CTaxon2_data > GetById(TTaxId tax_id)

CConstRef< CTaxon2_data > LookupMerge(COrg_ref &inp_orgRef, string *psLog=0, TOrgRefStatus *pStatusOut=0)

Operators to edit gaps in sequences.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

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.

SStrictId_Tax::TId TTaxId

Taxon id type.

const CNcbiArguments & GetArguments(void) const

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

#define TAX_ID_FROM(T, value)

@ fHideLogfile

Hide log file description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

@ eNoOwnership

No ownership is assumed.

size_t GetNExtra(void) const

Get the number of unnamed positional (a.k.a. extra) args.

@ eRequires

One argument requires another.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

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

Set diagnostic stream.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

#define NCBI_USER_THROW_FMT(message)

Throw a "user exception" with message processed as output to ostream.

static CResult SpawnVP(EMode mode, const char *cmdname, const char *const *argv=NULL)

Spawn a new process with variable number of command-line arguments and find file to execute from the ...

static string QuoteArg(const string &arg)

Quote argument.

@ eWait

Suspends calling thread until execution of new process is complete (synchronous operation).

virtual bool Exists(void) const

Check existence of file.

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

Set object to copy of another one.

#define MSerial_AsnText

I/O stream manipulators â.

ESerialDataFormat

Data file format.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

pair< TObjectPtr, TTypeInfo > ObjectInfo(C &obj)

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CConstRef< CSeq_entry > GetCompleteSeq_entry(void) const

Complete and get const reference to the seq-entry.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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

Convert int to string.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

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.

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

void SetOrg(TOrg &value)

Assign a value to Org data member.

void SetName(const TName &value)

Assign a value to Name data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

void SetTag(TTag &value)

Assign a value to Tag data member.

void SetDb(const TDb &value)

Assign a value to Db data member.

const TMod & GetMod(void) const

Get the Mod member data.

vector< CRef< CDbtag > > TDb

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TDb & GetDb(void) const

Get the Db member data.

void SetTaxname(const TTaxname &value)

Assign a value to Taxname data member.

list< CRef< COrgMod > > TMod

void SetOrgname(TOrgname &value)

Assign a value to Orgname data member.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

TSub & SetSub(void)

Select the variant.

TGeneral & SetGeneral(void)

Select the variant.

const TSeq & GetSeq(void) const

Get the variant data.

const TDescr & GetDescr(void) const

Get the Descr member data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSeq(void) const

Check if variant Seq is selected.

bool IsSet(void) const

Check if variant Set is selected.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

list< CRef< CSeq_entry > > TSeq_set

TSeq & SetSeq(void)

Select the variant.

list< CRef< CSeqdesc > > Tdata

TId & SetId(void)

Assign a value to Id data member.

void SetPub(TPub &value)

Assign a value to Pub data member.

TTitle & SetTitle(void)

Select the variant.

TPub & SetPub(void)

Select the variant.

void ResetAnnot(void)

Reset Annot data member.

const Tdata & Get(void) const

Get the member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

TSource & SetSource(void)

Select the variant.

void SetDescr(TDescr &value)

Assign a value to Descr data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

@ eRepr_raw

continuous sequence

const TCit & GetCit(void) const

Get the Cit member data.

void SetSub(TSub &value)

Assign a value to Sub data member.

const TEntrys & GetEntrys(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TSub & GetSub(void) const

Get the Sub member data.

bool IsEntrys(void) const

Check if variant Entrys is selected.

TIs_species_level GetIs_species_level(void) const

Get the Is_species_level member data.

void SetOrg(TOrg &value)

Assign a value to Org data member.

const TOrg & GetOrg(void) const

Get the Org member data.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

Defines a portable execute class.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Defines: CTimeFormat - storage class for time format.

@ eError

An error was encountered while trying to send request or to read and to process the reply.

#define DEFINE_STATIC_ARRAY_MAP(Type, Var, Array)

bool operator()(CRef< COrgMod > mod)

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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

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