NCBI C++ ToolKit
tblastn_vdb.cpp
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1 /* $Id: tblastn_vdb.cpp 101102 2023-10-30 13:07:22Z fongah2 $
2  * ===========================================================================
3  *
4  * PUBLIC DOMAIN NOTICE
5  * National Center for Biotechnology Information
6  *
7  * This software/database is a "United States Government Work" under the
8  * terms of the United States Copyright Act. It was written as part of
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11  * to the public for use. The National Library of Medicine and the U.S.
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15  * and reliability of the software and data, the NLM and the U.S.
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20  * purpose.
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22  * Please cite the author in any work or product based on this material.
23  *
24  * ===========================================================================
25  *
26  * Author: Amelia Fong
27  *
28  */
29 
30 /// @file blastn_vdb.cpp
31 /// BLASTN command line application that searches the vdb databases.
32 ///
33 /// - Based on the standard BLASTN command line application located in
34 /// app/blast/blastn_app.cpp.
35 /// - Modifications include using the VDB Blast utils class to
36 /// initialize VDB-specific BlastSeqSrc and BlastSeqInfoSrc objects.
37 /// - Does not support remote searches
38 
39 #include <ncbi_pch.hpp>
40 #include <corelib/ncbiapp.hpp>
46 
51 
52 #include "blast_vdb_app_util.hpp"
53 #include "../blast/blast_app_util.hpp"
54 
55 #include "CBlastVdbVersion.hpp" // CBlastVdbVersion
56 
58 USING_SCOPE(blast);
60 
61 // ==========================================================================//
62 
63 /// Exit code for successful completion of the Blast search.
64 #define BLAST_SRA_EXIT_SUCCESS 0
65 /// Exit code for a Blast input error (in query/options).
66 #define BLAST_SRA_INPUT_ERROR 1
67 /// Exit code for a Blast engine-related error.
68 #define BLAST_SRA_ENGINE_ERROR 2
69 /// Exit code for all other errors and unknown exceptions.
70 #define BLAST_SRA_UNKNOWN_ERROR 255
71 
72 // ==========================================================================//
73 
74 /// CVDBTblastnApp
75 ///
76 /// Blastn application that searches the SRA databases.
77 
79 {
80 public:
81  /// Constructor, sets up the version info.
83 
85 
86 private:
87  /// Initialize the application.
88  virtual void Init(void);
89  /// Run the application.
90  virtual int Run(void);
91  /// Cleanup on application exit.
92  virtual void Exit(void);
93 
94  void x_SetupLocalVDBSearch();
95  void x_FillVDBInfo(CBlastFormatUtil::SDbInfo & vecDbInfo);
96 
98  void x_GetFullVDBPaths(void);
99 
100 private:
101  string m_dbAllNames;
103 
104  /// This application's command line arguments.
108 };
109 
110 // ==========================================================================//
111 // Various helper functions
112 
115 }
116 
117 
119 {
120  // Read the SRA-related input
121  const CArgs& args = GetArgs();
122  unsigned int num_threads = (unsigned int) (args[kArgNumThreads].AsInteger());
124  CLocalVDBBlast::PreprocessDBs(m_localVDBStruct, m_dbAllNames, num_threads, search_mode);
125 }
126 
127 void CVDBTblastnApp::x_FillVDBInfo(CBlastFormatUtil::SDbInfo & dbInfo )
128 {
129  dbInfo.is_protein = false;
130  dbInfo.name = m_dbAllNames;
131  dbInfo.definition = dbInfo.name;
132  dbInfo.total_length = m_localVDBStruct.total_length;
133  dbInfo.number_seqs = m_localVDBStruct.total_num_seqs;
134 }
135 
136 // ==========================================================================//
137 // Initialization
138 
140 {
142  version->SetVersionInfo(new CBlastVdbVersion);
144  m_StopWatch.Start();
145  if (m_UsageReport.IsEnabled()) {
147  }
148 
149 }
150 
152 {
154 
155  // read the command line
156 
159  SetEnvironment("CSRA_CLIP_BY_QUALITY", "true");
160  SetEnvironment("CSRA_PATH_IN_ID", "false");
161  //SetDiagTrace(eDT_Enable);
162 
163 }
164 
165 // ==========================================================================//
166 // Run demo
167 
169 {
171  vector<string> paths;
172  CVDBAliasUtil::FindVDBPaths(dbs, false, paths, NULL, NULL, true, true, false);
173  m_dbAllNames = NStr::Join(paths, " ");
174 }
175 
177 {
178  int status = BLAST_SRA_EXIT_SUCCESS;
179  try
180  {
181  // Allow the fasta reader to complain on invalid sequence input
183  SetDiagPostPrefix("tblastn_vdb");
184 
185  // Get the arguments
186  const CArgs& args = GetArgs();
187 
188  // Get and validate the Blast options
189  CRef<CBlastOptionsHandle> optsHandle;
191  optsHandle.Reset(&*m_CmdLineArgs->SetOptionsForSavedStrategy(args));
192  }
193  else {
194  if(!(args.Exist(kArgDb) && args[kArgDb]))
195  NCBI_THROW(CInputException, eInvalidInput,
196  "Must specify at least one SRA/WGS database");
197 
198  optsHandle.Reset(&*m_CmdLineArgs->SetOptions(args));
199  }
200  const CBlastOptions& opt = optsHandle->GetOptions();
201 
202  // Get the query sequence(s)
203  CRef<CQueryOptionsArgs> query_opts =
206 
207 
208  // Resolve all vdb paths first
210 
211  // Initialize the object manager and the scope object
213 
215  // Setup for local vdb search
217  // Create the DBInfo entries for dbs being searched
218  vector< CBlastFormatUtil::SDbInfo > vecDbInfo(1);
219  x_FillVDBInfo(vecDbInfo[0]);
220 
221  bool bIncludeFilteredReads = args[kArgIncludeFilteredReads].AsBoolean();
222  // Get the formatting options and initialize the formatter
224  CBlastFormat formatter(opt, vecDbInfo,
225  fmt_args->GetFormattedOutputChoice(),
226  query_opts->GetParseDeflines(),
228  fmt_args->GetNumDescriptions(),
229  fmt_args->GetNumAlignments(),
230  *scope,
231  fmt_args->ShowGis(),
232  fmt_args->DisplayHtmlOutput(),
234  fmt_args->GetCustomOutputFormatSpec(),
235  true,
237 
238  // Begin Blast output
239  formatter.SetQueryRange(query_opts->GetRange());
240  formatter.SetLineLength(fmt_args->GetLineLength());
243  && args[kArgOutput].AsString() != "-")
244  formatter.SetBaseFile(args[kArgOutput].AsString());
245  formatter.PrintProlog();
246 
247  // Process the input
248  if (pssm.Empty()) {
249  SDataLoaderConfig dlconfig(query_opts->QueryIsProtein());
251  CBlastInputSourceConfig iconfig(dlconfig, query_opts->GetStrand(),
252  query_opts->UseLowercaseMasks(),
253  query_opts->GetParseDeflines(),
254  query_opts->GetRange(),
256  iconfig.SetQueryLocalIdMode();
259 
260  for (; !input.End(); formatter.ResetScopeHistory()) {
261  CRef<CBlastQueryVector> query_batch(input.GetNextSeqBatch(*scope));
262  CRef<IQueryFactory> queries(new CObjMgr_QueryFactory(*query_batch));
263  SaveSearchStrategy(args, m_CmdLineArgs, queries, optsHandle);
264 
265  // Run local Blast
266  CRef<CSearchResultSet> results;
267  CLocalVDBBlast local_vdb_blast(query_batch, optsHandle, m_localVDBStruct, bIncludeFilteredReads);
268  results = local_vdb_blast.Run();
269 
270 
271  if (fmt_args->ArchiveFormatRequested(args)){
272  formatter.WriteArchive(*queries, *optsHandle, *results);
273  }
274  else {
275  //CScope::TBioseqHandles handles;
276  //SortAndFetchSeqData(*results, scope, handles);
277  // Output the results
278  ITERATE(CSearchResultSet, result, *results) {
279  formatter.PrintOneResultSet(**result, query_batch);
280  }
281  }
282  }
284  }
285  else {
286  _ASSERT(pssm->HasQuery());
287  _ASSERT(pssm->GetQuery().IsSeq());
288  CRef<IQueryFactory> queries;
290  scope->AddTopLevelSeqEntry(pssm->SetQuery());
291 
292  CRef<CSeq_loc> sl(new CSeq_loc());
293  sl->SetWhole().Assign(*pssm->GetQuery().GetSeq().GetFirstId());
294 
295  CRef<CBlastSearchQuery> q(new CBlastSearchQuery(*sl, *scope));
296  query->AddQuery(q);
297  _ASSERT(query.NotEmpty());
298 
299  SaveSearchStrategy(args, m_CmdLineArgs, queries, optsHandle, pssm);
300 
301  CRef<CSearchResultSet> results;
302  CLocalVDBBlast local_vdb_blast(pssm, optsHandle, m_localVDBStruct, bIncludeFilteredReads);
303  results = local_vdb_blast.Run();
304 
305  if (fmt_args->ArchiveFormatRequested(args)){
306  formatter.WriteArchive(*pssm, *optsHandle, *results);
307  }
308  else {
309  CScope::TBioseqHandles handles;
310  SortAndFetchSeqData(*results, scope, handles);
311  // Output the results
312  ITERATE(CSearchResultSet, result, *results) {
313  formatter.PrintOneResultSet(**result, query);
314  }
315  }
316  }
317 
318  // End Blast output
319  formatter.PrintEpilog(opt);
321 
322  // Optional debug output
324  optsHandle->GetOptions().DebugDumpText(NcbiCerr, "BLAST options", 1);
325  }
327  }
328  catch (const CInputException& e) {
329  cerr << "BLAST query/options error: " << e.GetMsg() << endl;
330  status = BLAST_SRA_INPUT_ERROR;
331  }
332  catch (const CArgException& e) {
333  cerr << "Command line argument error: " << e.GetMsg() << endl;
334  status = BLAST_SRA_INPUT_ERROR;
335  }
336  catch (const CBlastException& e) {
337  cerr << "BLAST engine error: " << e.GetMsg() << endl;
338  status = BLAST_SRA_ENGINE_ERROR;
339  // Temporary fix to avoid vdb core dump during cleanup SB-1170
340  abort();
341  }
342  catch (const CException& e) {
343  cerr << "Error: " << e.GetMsg() << endl;
344  status = BLAST_SRA_UNKNOWN_ERROR;
345  }
346  catch (const exception& e) {
347  cerr << "Error: " << e.what() << endl;
348  status = BLAST_SRA_UNKNOWN_ERROR;
349  }
350  catch (...) {
351  cerr << "Unknown exception occurred" << endl;
352  status = BLAST_SRA_UNKNOWN_ERROR;
353  }
354 
357  m_UsageReport.AddParam(CBlastUsageReport::eProgram, (string) "tblastn_vdb");
358  return status;
359 }
360 
361 // ==========================================================================//
362 // Cleanup
363 
365 {
366  SetDiagStream(0);
367 }
368 
369 // ==========================================================================//
370 // Main
371 
372 #ifndef SKIP_DOXYGEN_PROCESSING
373 int main(int argc, const char* argv[])
374 {
375  // Execute main application function
376  return CVDBTblastnApp().AppMain(argc, argv, 0, eDS_Default, "");
377 }
378 #endif /* SKIP_DOXYGEN_PROCESSING */
379 
380 // ==========================================================================//
Produce formatted blast output for command line applications.
void SaveSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args, CRef< blast::IQueryFactory > queries, CRef< blast::CBlastOptionsHandle > opts_hndl, CRef< objects::CPssmWithParameters > pssm, unsigned int num_iters)
Save the search strategy corresponding to the current command line search.
bool RecoverSearchStrategy(const CArgs &args, blast::CBlastAppArgs *cmdline_args)
Recover search strategy from input file.
string GetCmdlineArgs(const CNcbiArguments &a)
void LogQueryInfo(CBlastUsageReport &report, const CBlastInput &q_info)
Interface for reading SRA sequences into blast input.
CRef< CScope > GetVDBScope(string dbAllNames)
void SortAndFetchSeqData(const blast::CSearchResultSet &results, CRef< CScope > scope, CScope::TBioseqHandles &handles)
Utility functions for BLAST VDB command line applications.
const string kArgSRASearchMode
const string kArgIncludeFilteredReads
CArgException –.
Definition: ncbiargs.hpp:120
CArgs –.
Definition: ncbiargs.hpp:379
const CSeq_id * GetFirstId() const
Definition: Bioseq.cpp:271
CRef< CBlastOptionsHandle > SetOptionsForSavedStrategy(const CArgs &args)
Combine the command line arguments into a CBlastOptions object recovered from saved search strategy.
virtual CNcbiIstream & GetInputStream()
Get the input stream.
size_t GetNumThreads() const
Get the number of threads to spawn.
CRef< CBlastOptionsHandle > SetOptions(const CArgs &args)
Extract the command line arguments into a CBlastOptionsHandle object.
CRef< CBlastDatabaseArgs > GetBlastDatabaseArgs() const
Get the BLAST database arguments.
CArgDescriptions * SetCommandLine()
Set the command line arguments.
bool ExecuteRemotely() const
Determine whether the search should be executed remotely or not.
CRef< CQueryOptionsArgs > GetQueryOptionsArgs() const
Get the options for the query sequence(s)
CRef< CFormattingArgs > GetFormattingArgs() const
Get the formatting options.
bool ProduceDebugOutput() const
Return whether debug (verbose) output should be produced on remote searches (only available when comp...
virtual CNcbiOstream & GetOutputStream()
Get the output stream.
string GetDatabaseName() const
Get the BLAST database name.
Definition: blast_args.hpp:931
Defines BLAST error codes (user errors included)
Class representing a text file containing sequences in fasta format.
This class formats the BLAST results for command line applications.
void LogBlastSearchInfo(blast::CBlastUsageReport &report)
void PrintOneResultSet(const blast::CSearchResults &results, CConstRef< blast::CBlastQueryVector > queries, unsigned int itr_num=numeric_limits< unsigned int >::max(), blast::CPsiBlastIterationState::TSeqIds prev_seqids=blast::CPsiBlastIterationState::TSeqIds(), bool is_deltablast_domain_result=false)
Print all alignment information for a single query sequence along with any errors or warnings (errors...
void PrintEpilog(const blast::CBlastOptions &options)
Print the footer of the blast report.
void SetBaseFile(string base)
For use by XML2 only.
void ResetScopeHistory()
Resets the scope history for some output formats.
void SetLineLength(size_t len)
Set Alignment Length.
void WriteArchive(blast::IQueryFactory &queries, blast::CBlastOptionsHandle &options_handle, const blast::CSearchResultSet &results, unsigned int num_iters=0, const list< CRef< objects::CBlast4_error > > &msg=list< CRef< objects::CBlast4_error > >())
Writes out the query and results as an "archive" format.
void PrintProlog()
Print the header of the blast report.
void SetQueryRange(const TSeqRange &query_range)
Set query range.
Class that centralizes the configuration data for sequences to be converted.
Definition: blast_input.hpp:48
void SetQueryLocalIdMode()
Append query-specific prefix codes to all generated local ids.
Generalized converter from an abstract source of biological sequence data to collections of blast inp...
Encapsulates ALL the BLAST algorithm's options.
Query Vector.
Definition: sseqloc.hpp:276
Search Query.
Definition: sseqloc.hpp:147
void AddParam(EUsageParams p, int val)
void DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const
Definition: ddumpable.cpp:56
virtual bool ArchiveFormatRequested(const CArgs &args) const
string GetCustomOutputFormatSpec() const
Retrieve for string that specifies the custom output format for tabular and comma-separated value.
EOutputFormat GetFormattedOutputChoice() const
Get the choice of formatted output.
@ eJson
JSON XInclude.
@ eXml2
XML2 XInclude.
TSeqPos GetNumAlignments() const
Number of alignments to show in traditional BLAST output.
bool ShowGis() const
Display the NCBI GIs in formatted output?
TSeqPos GetNumDescriptions() const
Number of one-line descriptions to show in traditional BLAST output.
size_t GetLineLength() const
bool DisplayHtmlOutput() const
Display HTML output?
Defines user input exceptions.
static string PreprocessDBs(CLocalVDBBlast::SLocalVDBStruct &local_vdb, const string db_names, unsigned int num_threads=kDisableThreadedSearch, ESRASearchMode seach_mode=eAligned)
CRef< CSearchResultSet > Run()
NCBI C++ Object Manager dependant implementation of IQueryFactory.
const CSeq_entry & GetQuery() const
Retrieve the query sequence.
CSeq_entry & SetQuery()
Retrieve the query sequence.
bool HasQuery() const
Has this PSSM a query in it?
objects::ENa_strand GetStrand() const
Get strand to search in query sequence(s)
Definition: blast_args.hpp:800
bool GetParseDeflines() const
Should the defline be parsed?
Definition: blast_args.hpp:804
bool QueryIsProtein() const
Is the query sequence protein?
Definition: blast_args.hpp:807
TSeqRange GetRange() const
Get query sequence range restriction.
Definition: blast_args.hpp:796
bool UseLowercaseMasks() const
Use lowercase masking in FASTA input?
Definition: blast_args.hpp:802
Search Results for All Queries.
CStopWatch –.
Definition: ncbitime.hpp:1938
Handles command line arguments for blastx binary.
virtual int GetQueryBatchSize() const
Get the query batch size.
CRef< objects::CPssmWithParameters > GetInputPssm() const
Get the PSSM.
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.
Definition: vdbalias.cpp:620
static Uint4 SetupVDBManager()
*Note* Call this in main thread first, if you are going to instantiate this object or use any of the ...
static void ReleaseVDBManager()
Call this release vdb manager if SetupManger has been explicitly called in the main thread.
CVDBTblastnApp.
Definition: tblastn_vdb.cpp:79
void x_GetFullVDBPaths(void)
CVDBTblastnApp()
Constructor, sets up the version info.
CLocalVDBBlast::SLocalVDBStruct m_localVDBStruct
virtual void Init(void)
Initialize the application.
CStopWatch m_StopWatch
virtual void Exit(void)
Cleanup on application exit.
virtual int Run(void)
Run the application.
void x_FillVDBInfo(CBlastFormatUtil::SDbInfo &vecDbInfo)
CRef< CTblastnVdbAppArgs > m_CmdLineArgs
This application's command line arguments.
CRef< CScope > x_GetScope(void)
CBlastUsageReport m_UsageReport
void x_SetupLocalVDBSearch()
const string kArgOutput
Output file name.
const string kArgDb
BLAST database name.
const string kArgNumThreads
Argument to determine the number of threads to use when running BLAST.
void Print(const CCompactSAMApplication::AlignInfo &ai)
const CBlastOptions & GetOptions() const
Return the object which this object is a handle for.
void SetFullVersion(CRef< CVersionAPI > version)
Set version data for the program.
Definition: ncbiapp.cpp:1174
void HideStdArgs(THideStdArgs hide_mask)
Set the hide mask for the Hide Std Flags.
Definition: ncbiapp.cpp:1312
CNcbiEnvironment & SetEnvironment(void)
Get a non-const copy of the application's cached environment.
virtual const CArgs & GetArgs(void) const
Get parsed command line arguments.
Definition: ncbiapp.cpp:305
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.
Definition: ncbiapp.cpp:819
CVersionInfo GetVersion(void) const
Get the program version information.
Definition: ncbiapp.cpp:1184
virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)
Setup the command line argument descriptions.
Definition: ncbiapp.cpp:1195
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
Definition: ncbimisc.hpp:815
const CNcbiArguments & GetArguments(void) const
Get the application's cached unprocessed command-line arguments.
@ fHideXmlHelp
Hide XML help description.
@ fHideLogfile
Hide log file description.
@ fHideFullVersion
Hide full version description.
@ fHideDryRun
Hide dryrun description.
@ fHideConffile
Hide configuration file description.
bool Exist(const string &name) const
Check existence of argument description.
Definition: ncbiargs.cpp:1813
#define NULL
Definition: ncbistd.hpp:225
void SetDiagPostPrefix(const char *prefix)
Specify a string to prefix all subsequent error postings with.
Definition: ncbidiag.cpp:6097
EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)
Set the threshold severity for posting the messages.
Definition: ncbidiag.cpp:6129
void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")
Set diagnostic stream.
Definition: ncbidiag.cpp:8083
@ eDS_Default
Try standard log file (app.name + ".log") in /log/, use stderr on failure.
Definition: ncbidiag.hpp:1790
@ eDiag_Warning
Warning message.
Definition: ncbidiag.hpp:652
#define NCBI_THROW(exception_class, err_code, message)
Generic macro to throw an exception, given the exception class, error code and message string.
Definition: ncbiexpt.hpp:704
const string & GetMsg(void) const
Get message string.
Definition: ncbiexpt.cpp:461
virtual const char * what(void) const noexcept
Standard report (includes full backlog).
Definition: ncbiexpt.cpp:342
void SetWhole(TWhole &v)
Definition: Seq_loc.hpp:982
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...
Definition: scope.cpp:522
vector< CBioseq_Handle > TBioseqHandles
Definition: scope.hpp:144
void Reset(void)
Reset reference object.
Definition: ncbiobj.hpp:773
bool Empty(void) const THROWS_NONE
Check if CRef is empty – not pointing to any object, which means having a null value.
Definition: ncbiobj.hpp:719
bool IsEnabled(void)
Indicates whether application usage statistics collection is enabled for a current reporter instance.
#define NcbiCerr
Definition: ncbistre.hpp:544
static string Join(const TContainer &arr, const CTempString &delim)
Join strings using the specified delimiter.
Definition: ncbistr.hpp:2697
double Elapsed(void) const
Return time elapsed since first Start() or last Restart() call (in seconds).
Definition: ncbitime.hpp:2776
void Start(void)
Start the timer.
Definition: ncbitime.hpp:2765
#define CVersion
const TSeq & GetSeq(void) const
Get the variant data.
Definition: Seq_entry_.cpp:102
bool IsSeq(void) const
Check if variant Seq is selected.
Definition: Seq_entry_.hpp:257
unsigned int
A callback function used to compare two keys in a database.
Definition: types.hpp:1210
static int input()
Main class to perform a BLAST search on the local machine.
static int version
Definition: mdb_load.c:29
Defines the CNcbiApplication and CAppException classes for creating NCBI applications.
void abort()
NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...
Declares the CRemoteBlast class.
Configuration structure for the CBlastScopeSource.
void OptimizeForWholeLargeSequenceRetrieval(bool value=true)
Configures the BLAST database data loader to optimize the retrieval of *entire* large sequences.
static string query
USING_SCOPE(blast)
#define BLAST_SRA_UNKNOWN_ERROR
Exit code for all other errors and unknown exceptions.
Definition: tblastn_vdb.cpp:70
#define BLAST_SRA_EXIT_SUCCESS
Exit code for successful completion of the Blast search.
Definition: tblastn_vdb.cpp:64
#define BLAST_SRA_ENGINE_ERROR
Exit code for a Blast engine-related error.
Definition: tblastn_vdb.cpp:68
#define BLAST_SRA_INPUT_ERROR
Exit code for a Blast input error (in query/options).
Definition: tblastn_vdb.cpp:66
int main(int argc, const char *argv[])
USING_NCBI_SCOPE
Definition: tblastn_vdb.cpp:57
#define _ASSERT
else result
Definition: token2.c:20
Defines database alias file access classes.
Declares the CLocalVDBBlast class.
Modified on Tue Apr 23 07:40:40 2024 by modify_doxy.py rev. 669887