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

45

arg_desc->SetUsageContext

47 "Microbial Genome Submission Check Tool (subcheck) is for the validation of " 48 "genome records prior to submission to GenBank. It utilizes a series of " 49 "self-consistency checks as well as comparison of submitted annotations to " 50 "computed annotations. Some of specified computed annotations could be " 51 "pre-computed using BLAST and its modifications and tRNAscanSE. Currently " 52 "there is no specific tool for predicting rRNA annotations. Please use the " 53 "format specified in documentation" 58

(

"in"

"input_asn"

59 "input file in the ASN.1 format, must be either Seq-entry or Seq-submit"

62

arg_desc->AddOptionalKey

63

(

"out"

"output_asn"

64 "output file in the ASN.1 format, of the same type (Seq-entry or Seq-submit)"

69 "keep frameshifted sequences and make misc_features at the same time. Needs editing after run!"

);

71

arg_desc->AddOptionalKey

72

(

"inblast"

"blast_res_proteins"

73 "input file which contains the standard BLAST output results (ran with -IT option) " 74 "for all query proteins " 75 "sequences specified in the input genome against a protein database (recommended: bact_prot " 76 "database of Refseq proteins supplied with the distributed standalone version of this tool)"

79

arg_desc->AddOptionalKey

80

(

"inblastcdd"

"blast_res_cdd"

81 "input file which contains the standard BLAST output results for all query proteins " 82 "sequences specified in input_asn against the CDD database"

85

arg_desc->AddOptionalKey

86

(

"intrna"

"input_trna"

87 "input tRNAscan predictions in default output format, default value is <-in parameter>.nfsa.tRNA"

90

arg_desc->AddOptionalKey

91

(

"inrrna"

"input_rrna"

92 "input ribosomal RNA predictions (5S, 16S, 23S), see the manual for format, default value is <-in parameter>.nfsa.rRNA"

95

arg_desc->AddOptionalKey(

96 "parentacc"

"parent_genome_accession"

97 "Refseq accession of the genome which protein annotations need to be excluded from BLAST output results"

100

arg_desc->AddOptionalKey(

101 "inparents"

"InputParentsFile"

102 "contains a list of all protein accessions/GIs for each Refseq accession/GI"

105

arg_desc->AddOptionalKey(

106 "intagmap"

"InputTagMap"

107 "use the file to map tags in BLAST"

110

arg_desc->AddDefaultKey(

"infmt"

"InputFormat"

"format of input file"

112

arg_desc->SetConstraint

115

arg_desc->AddOptionalKey

116

(

"outTbl"

"OutputTblFile"

117 "name of file to write additional TBL output (/dev/null by default)"

120

arg_desc->AddOptionalKey

121

(

"outPartial"

"OutputFilePartial"

122 "name of the output file for reporting \"partial hit\" problems"

125

arg_desc->AddOptionalKey

126

(

"outOverlap"

"OutputFileOverlap"

127 "name of the output file for reporting overlap problems"

130

arg_desc->AddOptionalKey

131

(

"outRnaOverlap"

"OutputFileRnaOverlap"

132 "name of the output file for reporting RNA overlap problems"

135

arg_desc->AddOptionalKey

136

(

"outCompleteOverlap"

"OutputFileCompleteOverlap"

137 "name of the output file for reporting complete overlap problems"

140

arg_desc->AddOptionalKey

141

(

"outOther"

"OutputFileOther"

142 "name of the output file for reporting other problems"

145

arg_desc->AddDefaultKey(

"outfmt"

"OutputFormat"

"format of output file"

147

arg_desc->SetConstraint

151

arg_desc->AddDefaultKey(

152 "verbosity"

"Verbosity"

153 "Verbosity level threshold"

157

arg_desc->AddDefaultKey(

158 "small_tails_threshold"

"small_tails_threshold"

159 "the sum of the left and right tails outside the aligned region for " 160 "the given sum less than this threshold will make it \"small tails\""

163

arg_desc->AddDefaultKey(

164 "n_best_hit"

"n_best_hit"

165 "number of BLAST best hits imported for each sequence"

168

arg_desc->AddDefaultKey(

169 "m_eThreshold"

"m_eThreshold"

170 "only CDD hits below this threshold will be used for partial hit definition"

173

arg_desc->AddDefaultKey(

174 "m_entireThreshold"

"m_entireThreshold"

175 "at least this part of the query needs to be in the alignment to be considered for partial hit candidate"

178

arg_desc->AddDefaultKey(

179 "m_partThreshold"

"m_partThreshold"

180 "if aligned region with CDD is less than this threshold, this hit will be considered for partial hit candidate"

183

arg_desc->AddDefaultKey(

184 "m_rna_overlapThreshold"

"m_rna_overlapThreshold"

185 "if protein and RNA annotations overlapping more than that threshold, it will be reported"

188

arg_desc->AddDefaultKey(

189 "m_cds_overlapThreshold"

"m_cds_overlapThreshold"

190 "if CDS annotations overlapping more than that threshold, it will be reported"

193

arg_desc->AddDefaultKey(

194 "m_trnascan_scoreThreshold"

"m_trnascan_scoreThreshold"

195 "tRNA-scan predictions below that threshold are ignored"

198

arg_desc->AddDefaultKey(

199 "m_shortProteinThreshold"

"m_shortProteinThreshold"

200 "proteins shorter than that will be reported and removed"

242 string

base = args[

"in"

].AsString();

253

unique_ptr<CObjectIStream>

in 255

args[

"in"

].AsInputFile()));

268 NcbiCerr

"WARNING: tbl file will be read but nothing more will be done."

NcbiEndl

;

269 if

m_tbl

Read

(args[

"in"

].AsInputFile()))

271 NcbiCerr

"FATAL: tbl file does not have any records or have been corrupted"

NcbiEndl

;

279 NcbiCerr

"FATAL: only tbl, Seq-submit or Seq-entry formats are accepted at this time. Seq-set has to be present as well"

NcbiEndl

;

299 if

( args[

"out"

HasValue

() &&

false

)

301

unique_ptr<CObjectOStream>

out 303

args[

"out"

].AsOutputFile()));

311 if

(args[

"intagmap"

HasValue

())

319 if

(args[

"parentacc"

HasValue

())

325 if

(args[

"inparents"

HasValue

())

336 if

ReadBlast

(args[

"inblast"

].AsString().c_str(), blastMap))

345 if

(args[

"inblastcdd"

HasValue

())

349 ReadBlast

(args[

"inblastcdd"

].AsString().c_str(), cddMap);

358

tRNA_file = args[

"intrna"

].AsString();

363

tRNA_file +=

".nfsa.tRNA"

;

374

rRNA_file =args[

"inrrna"

].AsString();

379

rRNA_file +=

".nfsa.rRNA"

;

411 NcbiCerr

"Dumping FASTA file for subsequent HTML blast output..."

NcbiEndl

;

416 bool

report_and_forget =

false

;

419 string

sout = args[

"outPartial"

].HasValue() ?

420

args[

"outPartial"

].AsString() :

421

base +

".partial.problems.log"

;

433 string

sout = args[

"outOverlap"

].HasValue() ?

434

args[

"outOverlap"

].AsString() :

435

base +

".overlap.problems.log"

;

447 string

sout = args[

"outRnaOverlap"

].HasValue() ?

448

args[

"outRnaOverlap"

].AsString() :

449

base +

".rna.overlap.problems.log"

;

462 string

sout = args[

"outCompleteOverlap"

].HasValue() ?

463

args[

"outCompleteOverlap"

].AsString() :

464

base +

".complete.overlap.problems.log"

;

468

"(eCompleteOverlap)" 476 string

sout = base +

".overlap.resolved.problems.log"

;

480

"(eRemoveOverlap)" 488 string

sout = base +

".tRNA.missing.log"

;

502 string

sout = base +

".tRNA.bad.strand.log"

;

506

"(eTRNABadStrand)" 514 string

sout = base +

".tRNA.undef.strand.log"

;

518

"(eTRNAUndefStrand)" 526 string

sout = base +

".tRNA.complete.mismatch.log"

;

530

"(eTRNAComMismatch)" 538 string

sout = base +

".tRNA.mismatch.log"

;

550 string

sout = base +

".short.annotation.log"

;

566 string

sout = args[

"outOther"

].HasValue() ?

567

args[

"outOther"

].AsString() :

568

base +

".frameshifts.problems.log"

;

572

"(eRelFrameShift)" 606

args[

"out"

].AsOutputFile().seekp(0);

607

unique_ptr<CObjectOStream>

out 609

args[

"out"

].AsOutputFile()));

void printGeneralInfo(ostream &out=NcbiCerr)

int CollectFrameshiftedSeqs(map< string, string > &problem_names)

static int m_verbosity_threshold

static bool PrintDetails(int current_verbosity=m_current_verbosity)

map< string, string > m_tagmap

static stack< int > m_saved_verbosity

list< long > m_previous_genome

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

int ReadRRNA2(const string &file)

static double m_trnascan_scoreThreshold

int simple_overlaps(void)

static int m_current_verbosity

bool ReadPreviousAcc(const string &file, list< long > &input_acc)

int RemoveProblems(map< string, string > &problem_seqs, LocMap &loc_map)

virtual void Init(void)

Initialize the application.

static int m_cds_overlapThreshold

int CopyInfoFromGenesToProteins(void)

===========================================================================

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

static double m_entireThreshold

static int m_rna_overlapThreshold

static ECoreDataType getCoreDataType(istream &in)

virtual int Run(void)

Run the application.

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

int AnalyzeSeqsViaBioseqs(bool in_pool_prot, bool against_prot)

TSimpleSeqs m_extRNAtable2

int ReadTagMap(const char *file)

int ReadParents(CNcbiIstream &in, const list< long > &nacc)

static bool less_simple_seq(const TSimpleSeq &first, const TSimpleSeq &second)

static int m_shortProteinThreshold

static void PopVerbosity(void)

ECoreDataType m_coreDataType

void reportProblems(const bool report_and_forget, diagMap &diag, ostream &out, const CBioseq::TAnnot &annots, const EProblem type)

static double m_small_tails_threshold

static double m_partThreshold

static double m_eThreshold

void dump_fasta_for_pretty_blast(diagMap &diag)

int ReadTRNA2(const string &file)

static void PushVerbosity(void)

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

main entry point for tests

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

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

string & Print(string &str) const

Print (append) all arguments to the string "str" and return "str".

@ fPreOpen

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

@ eInputFile

Name of file (must exist and be readable)

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

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

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

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

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

@ eOverlap

CSeq_locs overlap.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

void SetData(TData &value)

Assign a value to Data data member.

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

ESerialDataFormat s_GetFormat(const string &name)

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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/read__blast__result_8cpp_source.html below:

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

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/readblastresult_8cpp_source.html below: