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

138

: m_VdbBlastDB(sraobj), m_Out(

out

), m_FmtSpec(fmt_spec), m_LineWidth(line_width), m_FastaOnly(

false

), m_LoadSeq(

false

)

162 "Invalid format specification"

);

180 if

(bioseq.

Empty

()) {

189

fasta.

Write

(*bioseq);

200 ERR_POST

(

"Bioseq constains no sequence data"

);

221 m_Out

id

->GetSeqIdString(

true

);

227 m_Out

id

->AsFastaString() ;

252 if

(

.IsSetLength()){

260

os <<

"Unrecognized format specification: '%"

m_ReplTypes

[

] <<

"'"

;

278 ERR_POST

(

"Iterator returns BLAST_SEQSRC_ERROR"

);

282 if

(bioseq.

Empty

()) {

286

fasta.

Write

(*bioseq);

292 ERR_POST

(

"Iterator returns BLAST_SEQSRC_ERROR"

);

296 if

(bioseq.

Empty

()) {

306 string s_GetCSRADBs

(

const string

& db_list,

string

& not_csra_list) {

311 for

(

unsigned int i

=0;

< dbs.size();

++) {

313

csra_list += dbs[

] +

" "

;

316

not_csra_list += dbs[

] +

" "

;

326

vector<string> retval;

330 static const string

kDelim(

","

);

331 const string

& entry = args[

"entry"

].AsString();

333 if

(entry.find(kDelim[0]) != string::npos) {

334

vector<string> tokens;

338

retval.push_back(entry);

341

}

else if

(args[

"entry_batch"

HasValue

()) {

348 if

( !line.empty() ) {

349

retval.push_back(line);

354 "Must specify query type: one of 'entry', or 'entry_batch'"

);

357 if

(retval.empty()) {

359 "Entry not found in BLAST database"

);

371 bool

errors_found =

false

;

374 if

(args[

"entry"

HasValue

() && args[

"entry"

].AsString() ==

"all"

) {

381

errors_found =

true

;

384

errors_found =

true

;

386 return

errors_found ? 1 : 0;

398

seq_fmt_csra =

new CVdbFastaExtractor

(util_csra,

out

, args[

"outfmt"

].AsString(), args[

"line_length"

].AsInteger());

407

*itr =

"SRA:"

+ *itr;

413

seq_fmt.

Write

(seq_id);

418 if

(seq_fmt_csra ==

NULL

) {

421

seq_fmt_csra->

Write

(seq_id);

431

errors_found =

true

;

433 ERR_POST

(

"Failed to retrieve requested item"

);

434

errors_found =

true

;

438 if

(seq_fmt_csra !=

NULL

) {

441 return

errors_found ? 1 : 0;

456

strAllRuns = args[

"db"

].AsString();

465

strAllRuns += line +

" "

;

478 if

(args[

"include_filtered_reads"

]) {

487

vector<string> vdb_alias;

488

vector<string> db_alias;

523

list<string> print_str;

525 ITERATE

(list<string>, itr, print_str) {

533 const string

kLetters(

"bases"

);

536 unsigned int

line_width = args[

"line_length"

].AsInteger();

537 Uint8

num_seqs(0), length(0), max_seq_length(0), av_seq_length(0);

538 Uint8

ref_num_seqs(0), ref_length(0);

550 out

"Database(s): "

;

559 out

"Database(s) Full Path: "

;

560 if

(

m_allDbs

.size() > line_width) {

574 out

"CSRA Database(s): "

;

575 if

(csra_dbs.size() > line_width) {

580 out

<< csra_dbs << endl;

597

vector<string> vdb_alias;

598

vector<string> db_alias;

608 out

"None"

<< endl;

612 ITERATE

(vector<string>, itr, vdbs)

617 out

"VDB Alias File(s): "

;

618 if

(vdb_alias.empty()) {

619 out

"None"

<< endl;

623 ITERATE

(vector<string>, itr, vdb_alias)

627 out

"Blats DB Alias File(s): "

;

628 if

(db_alias.empty()) {

629 out

"None"

<< endl;

633 ITERATE

(vector<string>, itr, db_alias)

648

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

"BLAST-VDB Cmd"

);

651

arg_desc->SetCurrentGroup(

"VDB 'BLASTDB' options"

);

652

arg_desc->AddKey(

"db"

"VDB_ACCESSIONS"

653 "List of whitespace-separated VDB accessions"

655

arg_desc->AddKey(

"dbs_file"

"Input_File_with_VDB_ACCESSIONS"

656 "File with a newline delimited list of VDB Run accessions"

661

arg_desc->AddDefaultKey(

"outfmt"

"format"

662 "Output format, where the available format specifiers are:\n" 663 "\t\t%f means sequence in FASTA format\n" 664 "\t\t%s means sequence data (without defline)\n" 665 "\t\t%a means accession\n" 666 "\t\t%o means ordinal id (OID)\n" 667 "\t\t%i means sequence id\n" 668 "\t\t%t means sequence title\n" 669 "\t\t%l means sequence length\n" 670 "\tFor every format except '%f', each line of output will " 671 "correspond\n\tto a sequence.\n"

674

arg_desc->SetCurrentGroup(

"Retrieval options"

);

675

arg_desc->AddOptionalKey(

"entry"

"sequence_identifier"

676 "Comma-delimited search string(s) of sequence identifiers" 677 ":\n\te.g.: 'gnl|SRR|SRR066117.18823.2', or 'all' " 678 "to select all\n\tsequences in the database"

680

arg_desc->AddOptionalKey(

"entry_batch"

"input_file"

681 "Input file for batch processing (Format: one entry per line)"

684

arg_desc->AddDefaultKey(

"line_length"

"number"

"Line length for output"

687

arg_desc->SetConstraint(

"line_length"

690

arg_desc->AddFlag(

"include_filtered_reads"

"Include Filtered reads"

true

);

693 const char

* exclusions[] = {

"entry"

"entry_batch"

};

694 for

(

size_t i

= 0;

sizeof

(exclusions)/

sizeof

(*exclusions);

++) {

698

arg_desc->AddFlag(

"info"

"Print VDB information"

true

);

699

arg_desc->AddFlag(

"ref"

700 "Dump reference seqs"

true

);

705

arg_desc->AddFlag(

"paths"

"Get top level paths"

true

);

706

arg_desc->AddFlag(

"paths_all"

"Get all vdb and alias paths"

true

);

707 const char

* exclude_paths[] = {

"scan_uncompressed"

"scan_compressed"

"info"

"entry"

"entry_batch"

"include_filtered_reads"

};

708 for

(

size_t i

= 0;

sizeof

(exclude_paths)/

sizeof

(*exclude_paths);

++) {

712

arg_desc->SetCurrentGroup(

"Output configuration options"

);

713

arg_desc->AddDefaultKey(

"out"

"output_file"

"Output file name"

732 if

(args[

"paths_all"

HasValue

()) {

738 if

(args[

"info"

]) {

741 else if

(args[

"entry"

HasValue

() || args[

"entry_batch"

HasValue

()) {

747

}

catch

(

const

exception& e) {

761 if

(args[

"info"

]) {

764 else if

(args[

"entry"

HasValue

() || args[

"entry_batch"

HasValue

()) {

766 if

(args[

"entry"

HasValue

() && args[

"entry"

].AsString() ==

"all"

) {

770 if

(args[

"outfmt"

HasValue

()) {

780 #ifndef SKIP_DOXYGEN_PROCESSING 781 int main

(

int

argc,

const char

* argv[]

)

Interface for converting sources of sequence data into blast sequence input.

Auxiliary classes/functions for BLAST input library.

#define BLAST_SEQSRC_ERROR

Error while retrieving sequence.

Int4 BlastSeqSrcIteratorNext(const BlastSeqSrc *seq_src, BlastSeqSrcIterator *itr)

Increments the BlastSeqSrcIterator.

BlastSeqSrcIterator * BlastSeqSrcIteratorNewEx(unsigned int chunk_sz)

Allocate and initialize an iterator over a BlastSeqSrc.

#define BLAST_SEQSRC_EOF

No more sequences available.

void s_PrintStr(const string &str, unsigned int line_width, CNcbiOstream &out)

string s_GetCSRADBs(const string &db_list, string &not_csra_list)

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

static const NStr::TNumToStringFlags kFlags

Class to constrain the values of an argument to those greater than or equal to the value specified in...

const CSeq_id * GetFirstId() const

Defines BLAST error codes (user errors included)

void AddParam(EUsageParams p, int val)

string x_FormatRuntime(const CStopWatch &sw) const

int x_PrintVDBPaths(bool recursive)

Print vdb paths.

void x_InitApplicationData()

Initializes the application's data members.

virtual void Init()

@inheritDoc

CBlastUsageReport m_UsageReport

CBlastVdbCmdApp()

@inheritDoc

int x_ProcessSearchRequest()

Processes all requests except printing the BLAST database information.

CRef< CVDBBlastUtil > x_GetVDBBlastUtil(bool isCSRA)

Get vdb util.

int x_PrintBlastDatabaseInformation()

Prints the BLAST database information (e.g.

vector< string > x_GetQueries()

Retrieve the queries from the command line arguments.

void x_GetFullPaths()

Resolve vdb paths.

virtual int Run()

@inheritDoc

bool m_includeFilteredReads

Keeps track of the version of the BLAST engine in the NCBI C++ toolkit.

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

Defines user input exceptions.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

static void FindVDBPaths(const string &dbname, bool isProtein, vector< string > &paths, vector< string > *db_alias_list=NULL, vector< string > *vdb_alias_list=NULL, bool recursive=true, bool expand_links=true, bool verify_dbs=true)

Get the list of vdb names.

BlastSeqSrc * GetSRASeqSrc()

Return the stored SRA BlastSeqSrc object.

Uint4 GetOIDFromVDBSeqId(CRef< objects::CSeq_id > seqId)

Get the ordinal number (OID) for the given SRA sequence.

static void GetVDBStats(const string &strAllRuns, Uint8 &num_seqs, Uint8 &length, bool getRefStats=false)

Fucntion to get around the OID (blastseqsrc) limit So num of seqs > int4 can be returned.

CRef< objects::CBioseq > CreateBioseqFromVDBSeqId(CRef< objects::CSeq_id > seqId)

Construct a Bioseq object for the given SRA sequence.

static bool IsCSRA(const string &db_name)

CRef< objects::CBioseq > CreateBioseqFromOid(Uint8 oid)

static IDType VDBIdType(const CSeq_id &id)

void Print(const CCompactSAMApplication::AlignInfo &ai)

static const char si[8][64]

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

main entry point for tests

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

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

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.

CVersionInfo GetVersion(void) const

Get the program version information.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

#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.

const CNcbiArguments & GetArguments(void) const

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

@ fHideXmlHelp

Hide XML help description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

void SetDiagPostPrefix(const char *prefix)

Specify a string to prefix all subsequent error postings with.

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.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

@ eDS_Default

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

@ eDiag_Warning

Warning message.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

const TPrim & Get(void) const

const string AsFastaString(void) const

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

void SetWidth(TSeqPos width)

void SetAllFlags(TFlags flags)

@ fNoExpensiveOps

don't try too hard to find titles

@ fKeepGTSigns

don't convert '>' to '_' in title

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

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

bool Empty(void) const THROWS_NONE

Check if CRef is empty â not pointing to any object, which means having a null value.

uint64_t Uint8

8-byte (64-bit) unsigned integer

bool IsEnabled(void)

Indicates whether application usage statistics collection is enabled for a current reporter instance.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

CNcbiIstream & NcbiGetline(CNcbiIstream &is, string &str, char delim, string::size_type *count=NULL)

Read from "is" to "str" up to the delimiter symbol "delim" (or EOF)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

NCBI_NS_STD::string::size_type SIZE_TYPE

int TNumToStringFlags

Bitwise OR of "ENumToStringFlags".

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

Join strings using the specified delimiter.

static string ULongToString(unsigned long value, TNumToStringFlags flags=0, int base=10)

Convert unsigned long to string.

static void Wrap(const string &str, SIZE_TYPE width, IWrapDest &dest, TWrapFlags flags, const string *prefix, const string *prefix1)

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.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ fWithCommas

Use commas as thousands separator.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Stop(void)

Suspend the timer.

string AsSmartString(CTimeSpan::ESmartStringPrecision precision, ERound rounding, CTimeSpan::ESmartStringZeroMode zero_mode=CTimeSpan::eSSZ_SkipZero) const

Transform elapsed time to "smart" string.

void Start(void)

Start the timer.

bool IsSetSeq_data(void) const

the sequence Check if a value has been assigned to Seq_data data member.

const TInst & GetInst(void) const

Get the Inst member data.

const TIupacna & GetIupacna(void) const

Get the variant data.

const TTitle & GetTitle(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

bool IsSetDescr(void) const

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

bool IsSet(void) const

Check if a value has been assigned to data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

bool IsIupacna(void) const

Check if variant Iupacna is selected.

unsigned int

A callback function used to compare two keys in a database.

const string version

version string

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

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

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Structure used as the second argument to functions satisfying the GetSeqBlkFnPtr signature,...

Int4 oid

Oid in BLAST database, index in an array of sequences, etc [in].

Complete type definition of Blast Sequence Source Iterator.

Complete type definition of Blast Sequence Source ADT.

Defines database alias file access classes.

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Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blast__vdb__cmd_8cpp_source.html below:

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/blastvdbcmd_8cpp_source.html below: