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  C++/include/objtools/align_format/tabular.hpp


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/* $Id: tabular.hpp 72912 2016-06-07 17:51:40Z jianye $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's offical duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Ilya Dondoshansky * * =========================================================================== */ /// @file: tabular.hpp /// Formatting of pairwise sequence alignments in tabular form. #ifndef OBJTOOLS_ALIGN_FORMAT___TABULAR_HPP #define OBJTOOLS_ALIGN_FORMAT___TABULAR_HPP #include <corelib/ncbistre.hpp> #include <objects/seqalign/Seq_align.hpp> #include <objects/seqloc/Seq_id.hpp> #include <objmgr/scope.hpp> #include <objtools/align_format/align_format_util.hpp> #include <objtools/blast/seqdb_reader/seqdb.hpp> #include <algo/blast/igblast/igblast.hpp> #include <objects/blastdb/Blast_def_line_set.hpp> #include <algorithm> BEGIN_NCBI_SCOPE BEGIN_SCOPE(align_format) /// Class containing information needed for tabular formatting of BLAST /// results. class NCBI_ALIGN_FORMAT_EXPORT CBlastTabularInfo : public CObject { public: /// In what form should the sequence identifiers be shown? enum ESeqIdType { eFullId = 0, ///< Show full seq-id, with multiple ids concatenated. eAccession, ///< Show only best accession eAccVersion, ///< Show only best accession.version eGi ///< Show only gi }; /// What delimiter to use between fields in each row of the tabular output. enum EFieldDelimiter { eTab = 0, ///< Tab eSpace, ///< Space eComma ///< Comma }; /// Constructor /// @param ostr Stream to write output to [in] /// @param format Output format - what fields to include in the output [in] /// @param delim Delimiter to use between tabular fields [in] /// @note fields that are not recognized will be ignored, if no fields are /// specified (or left after purging those that are not recognized), the /// default format is assumed CBlastTabularInfo(CNcbiOstream& ostr, const string& format = kDfltArgTabularOutputFmt, EFieldDelimiter delim = eTab, bool parse_local_ids = false); /// Destructor ~CBlastTabularInfo(); /// Set query id from a objects::CSeq_id /// @param id List of Seq-ids to use [in] void SetQueryId(list<CRef<objects::CSeq_id> >& id); /// Set query id from a Bioseq handle /// @param bh Bioseq handle to get Seq-ids from void SetQueryId(const objects::CBioseq_Handle& bh); /// Set subject id from a objects::CSeq_id /// @param id List of Seq-ids to use [in] void SetSubjectId(list<CRef<objects::CSeq_id> >& id); /// Set subject id from a Bioseq handle /// @param bh Bioseq handle to get Seq-ids from void SetSubjectId(const objects::CBioseq_Handle& bh); /// Set the HSP scores /// @param score Raw score [in] /// @param bit_score Bit score [in] /// @param evalue Expect value [in] void SetScores(int score, double bit_score, double evalue); /// Set the HSP endpoints. Note that if alignment is on opposite strands, /// the subject offsets must be reversed. /// @param q_start Starting offset in query [in] /// @param q_end Ending offset in query [in] /// @param s_start Starting offset in subject [in] /// @param s_end Ending offset in subject [in] void SetEndpoints(int q_start, int q_end, int s_start, int s_end); /// Set various counts/lengths /// @param num_ident Number of identities [in] /// @param length Alignment length [in] /// @param gaps Total number of gaps [in] /// @param gap_opens Number of gap openings [in] /// @param positives Number of positives [in] void SetCounts(int num_ident, int length, int gaps, int gap_opens, int positives =0, int query_frame = 1, int subject_frame = 1); /// Sets the Blast-traceback-operations string. /// @param btop_string string for blast traceback operations [in] void SetBTOP(string btop_string); /// Set all member fields, given a Seq-align /// @param sal Seq-align to get data from [in] /// @param scope Scope for Bioseq retrieval [in] /// @param matrix Matrix to calculate positives; NULL if not applicable. [in] /// @return 0 on success, 1 if query or subject Bioseq is not found. int SetFields(const objects::CSeq_align& sal, objects::CScope& scope, CNcbiMatrix<int>* matrix=0); /// Print one line of tabular output virtual void Print(void); /// Print the tabular output header /// @param program Program name to show in the header [in] /// @param bioseq Query Bioseq [in] /// @param dbname Search database name [in] /// @param rid the search RID (if not applicable, it should be empty /// the string) [in] /// @param iteration Iteration number (for PSI-BLAST), use default /// parameter value when not applicable [in] /// @param align_set All alignments for this query [in] void PrintHeader(const string& program, const objects::CBioseq& bioseq, const string& dbname, const string& rid = kEmptyStr, unsigned int iteration = numeric_limits<unsigned int>::max(), const objects::CSeq_align_set* align_set=0, CConstRef<objects::CBioseq> subj_bioseq = CConstRef<objects::CBioseq>()); /// Prints number of queries processed. /// @param num_queries number of queries processed [in] void PrintNumProcessed(int num_queries); /// Return all field names supported in the format string. list<string> GetAllFieldNames(void); /// Should local IDs be parsed or not? /// @param val value to set [in] /// Returns true if the field was requested in the format specification /// @param field Which field to test [in] void SetParseLocalIds(bool val) { m_ParseLocalIds = val; } /// Should subject deflien be parsed for id or not? /// @param val value to set [in] void SetParseSubjectDefline(bool val) { m_ParseSubjectDefline = val; } /// Avoid fetching sequence (if possible) /// If the sequence is needed (e.g., will be formatted, it will be fetched) /// @param nofetch Do not fetch if true [in] void SetNoFetch(bool nofetch); /// Avoid fetch of sequence if true returned bool GetNoFetch(); // Set Genetic code for translating seqs void SetQueryGeneticCode(int q_gc) {m_QueryGeneticCode = q_gc;} void SetDbGeneticCode(int db_gc) {m_DbGeneticCode = db_gc;} /// Set query range /// @param query range [in] void SetQueryRange(TSeqRange & q_range) { m_QueryRange = q_range;} protected: bool x_IsFieldRequested(ETabularField field); /// Add a field to the list of fields to show, if it is not yet present in /// the list of fields. /// @param field Which field to add? [in] void x_AddFieldToShow(ETabularField field); /// Delete a field from the list of fields to show /// @param field Which field to delete? [in] void x_DeleteFieldToShow(ETabularField field); /// Add a default set of fields to show. void x_AddDefaultFieldsToShow(void); /// Set fields to show, given an output format string /// @param format Output format [in] void x_SetFieldsToShow(const string& format); /// Reset values of all fields. void x_ResetFields(void); /// Set the tabular fields delimiter. /// @param delim Which delimiter to use void x_SetFieldDelimiter(EFieldDelimiter delim); /// Print the names of all supported fields void x_PrintFieldNames(void); /// Print the value of a given field /// @param field Which field to show? [in] void x_PrintField(ETabularField field); /// Print query Seq-id void x_PrintQuerySeqId(void) const; /// Print query gi void x_PrintQueryGi(void); /// Print query accession void x_PrintQueryAccession(void); /// Print query accession.version void x_PrintQueryAccessionVersion(void); /// Print query and database names void x_PrintQueryAndDbNames(const string& program, const objects::CBioseq& bioseq, const string& dbname, const string& rid, unsigned int iteration, CConstRef<objects::CBioseq> subj_bioseq); /// Print subject Seq-id void x_PrintSubjectSeqId(void); /// Print all Seq-ids associated with this subject, separated by ';' void x_PrintSubjectAllSeqIds(void); /// Print subject gi void x_PrintSubjectGi(void); /// Print all gis associated with this subject, separated by ';' void x_PrintSubjectAllGis(void); /// Print subject accession void x_PrintSubjectAccession(void); /// Print subject accession.version void x_PrintSubjectAccessionVersion(void); /// Print all accessions associated with this subject, separated by ';' void x_PrintSubjectAllAccessions(void); /// Print aligned part of query sequence void x_PrintQuerySeq(void); /// Print aligned part of subject sequence void x_PrintSubjectSeq(void); /// Print query start void x_PrintQueryStart(void); /// Print query end void x_PrintQueryEnd(void); /// Print subject start void x_PrintSubjectStart(void); /// Print subject end void x_PrintSubjectEnd(void); /// Print e-value void x_PrintEvalue(void); /// Print bit score void x_PrintBitScore(void); /// Print raw score void x_PrintScore(void); /// Print alignment length void x_PrintAlignmentLength(void); /// Print percent of identical matches void x_PrintPercentIdentical(void); /// Print number of identical matches void x_PrintNumIdentical(void); /// Print number of mismatches void x_PrintMismatches(void); /// Print number of positive matches void x_PrintNumPositives(void); /// Print number of gap openings void x_PrintGapOpenings(void); /// Print total number of gaps void x_PrintGaps(void); /// Print percent positives void x_PrintPercentPositives(); /// Print frames void x_PrintFrames(); void x_PrintQueryFrame(); void x_PrintSubjectFrame(); void x_PrintBTOP(); /// Print the query sequence length void x_PrintQueryLength(); /// Print the subject sequence length void x_PrintSubjectLength(); /// Print subject tax info void x_PrintSubjectTaxIds(); void x_PrintSubjectSciNames(); void x_PrintSubjectCommonNames(); void x_PrintSubjectBlastNames(); void x_PrintSubjectSuperKingdoms(); void x_PrintSubjectTaxId(); void x_PrintSubjectSciName(); void x_PrintSubjectCommonName(); void x_PrintSubjectBlastName(); void x_PrintSubjectSuperKingdom(); void x_PrintSubjectTitle(); void x_PrintSubjectAllTitles(); void x_PrintSubjectStrand(); void x_PrintSeqalignCoverage(); void x_PrintSubjectCoverage(); void x_PrintUniqSubjectCoverage(); void x_SetTaxInfo(const objects::CBioseq_Handle & handle, const CRef<objects::CBlast_def_line_set> & bdlRef); void x_SetTaxInfoAll(const objects::CBioseq_Handle & handle, const CRef<objects::CBlast_def_line_set> & bdlRef); void x_SetSubjectIds(const objects::CBioseq_Handle& bh, const CRef<objects::CBlast_def_line_set> & bdlRef); void x_SetQueryCovSubject(const objects::CSeq_align & align); void x_SetQueryCovUniqSubject(const objects::CSeq_align & align); void x_SetQueryCovSeqalign(const CSeq_align & align, int query_len); void x_CheckTaxDB(); CNcbiOstream& m_Ostream; ///< Stream to write output to char m_FieldDelimiter; ///< Delimiter character for fields to print. string m_QuerySeq; ///< Aligned part of the query sequence string m_SubjectSeq; ///< Aligned part of the subject sequence int m_QueryStart; ///< Starting offset in query int m_QueryEnd; ///< Ending offset in query int m_QueryFrame; ///< query frame int m_SubjectStart; ///< Starting offset in subject int m_SubjectEnd; ///< Ending offset in subject int m_SubjectFrame; ///< subject frame bool m_NoFetch; ///< program as a string private: list<CRef<objects::CSeq_id> > m_QueryId; ///< List of query ids for this HSP list<CRef<objects::CSeq_id> > m_SubjectId; /// All subject sequence ids for this HSP vector<list<CRef<objects::CSeq_id> > > m_SubjectIds; TSeqPos m_QueryLength; ///< Length of query sequence TSeqPos m_SubjectLength; ///< Length of subject sequence int m_Score; ///< Raw score of this HSP string m_BitScore; ///< Bit score of this HSP, in appropriate format string m_Evalue; ///< E-value of this HSP, in appropriate format int m_AlignLength; ///< Alignment length of this HSP int m_NumGaps; ///< Total number of gaps in this HSP int m_NumGapOpens; ///< Number of gap openings in this HSP int m_NumIdent; ///< Number of identities in this HSP int m_NumPositives; ///< Number of positives in this HSP /// Map of field enum values to field names. map<string, ETabularField> m_FieldMap; list<ETabularField> m_FieldsToShow; ///< Which fields to show? /// Should the query deflines be parsed for local IDs? bool m_ParseLocalIds; /// Parse subejct defline? bool m_ParseSubjectDefline; string m_BTOP; /// Blast-traceback-operations. //TaxInfo set<int> m_SubjectTaxIds; vector<string> m_SubjectSciNames; vector<string> m_SubjectCommonNames; set<string> m_SubjectBlastNames; set<string> m_SubjectSuperKingdoms; int m_SubjectTaxId; string m_SubjectSciName; string m_SubjectCommonName; string m_SubjectBlastName; string m_SubjectSuperKingdom; CRef<CBlast_def_line_set> m_SubjectDefline; string m_SubjectStrand; pair<string, int> m_QueryCovSubject; pair<string, int> m_QueryCovUniqSubject; int m_QueryCovSeqalign; int m_QueryGeneticCode; int m_DbGeneticCode; TSeqRange m_QueryRange; }; inline void CBlastTabularInfo::x_PrintQuerySeq(void) { m_Ostream << m_QuerySeq; } inline void CBlastTabularInfo::x_PrintSubjectSeq(void) { m_Ostream << m_SubjectSeq; } inline void CBlastTabularInfo::x_PrintQueryStart(void) { m_Ostream << m_QueryStart; } inline void CBlastTabularInfo::x_PrintQueryEnd(void) { m_Ostream << m_QueryEnd; } inline void CBlastTabularInfo::x_PrintSubjectStart(void) { m_Ostream << m_SubjectStart; } inline void CBlastTabularInfo::x_PrintSubjectEnd(void) { m_Ostream << m_SubjectEnd; } inline void CBlastTabularInfo::x_PrintEvalue(void) { m_Ostream << m_Evalue; } inline void CBlastTabularInfo::x_PrintBitScore(void) { m_Ostream << m_BitScore; } inline void CBlastTabularInfo::x_PrintScore(void) { m_Ostream << m_Score; } inline void CBlastTabularInfo::x_PrintAlignmentLength(void) { m_Ostream << m_AlignLength; } inline void CBlastTabularInfo::x_PrintPercentIdentical(void) { double perc_ident = (m_AlignLength > 0 ? ((double)m_NumIdent)/m_AlignLength * 100 : 0); m_Ostream << NStr::DoubleToString(perc_ident, 3); } inline void CBlastTabularInfo::x_PrintPercentPositives(void) { double perc_positives = (m_AlignLength > 0 ? ((double)m_NumPositives)/m_AlignLength * 100 : 0); m_Ostream << NStr::DoubleToString(perc_positives, 2); } inline void CBlastTabularInfo::x_PrintFrames(void) { m_Ostream << m_QueryFrame << "/" << m_SubjectFrame; } inline void CBlastTabularInfo::x_PrintQueryFrame(void) { m_Ostream << m_QueryFrame; } inline void CBlastTabularInfo::x_PrintSubjectFrame(void) { m_Ostream << m_SubjectFrame; } inline void CBlastTabularInfo::x_PrintBTOP(void) { m_Ostream << m_BTOP; } inline void CBlastTabularInfo::x_PrintNumIdentical(void) { m_Ostream << m_NumIdent; } inline void CBlastTabularInfo::x_PrintMismatches(void) { int num_mismatches = m_AlignLength - m_NumIdent - m_NumGaps; m_Ostream << num_mismatches; } inline void CBlastTabularInfo::x_PrintNumPositives(void) { m_Ostream << m_NumPositives; } // FIXME; do this via a bit field inline bool CBlastTabularInfo::x_IsFieldRequested(ETabularField field) { return find(m_FieldsToShow.begin(), m_FieldsToShow.end(), field) != m_FieldsToShow.end(); } inline void CBlastTabularInfo::x_PrintGapOpenings(void) { m_Ostream << m_NumGapOpens; } inline void CBlastTabularInfo::x_PrintGaps(void) { m_Ostream << m_NumGaps; } inline void CBlastTabularInfo::x_PrintQueryLength(void) { m_Ostream << m_QueryLength; } inline void CBlastTabularInfo::x_PrintSubjectLength(void) { m_Ostream << m_SubjectLength; } inline void CBlastTabularInfo::SetNoFetch(bool nofetch) { m_NoFetch = nofetch; } inline bool CBlastTabularInfo::GetNoFetch(void) { return m_NoFetch; } /// Class containing information needed for tabular formatting of BLAST /// results. class NCBI_ALIGN_FORMAT_EXPORT CIgBlastTabularInfo : public CBlastTabularInfo { public: /// struct containing annotated domain information struct SIgDomain { SIgDomain(const string& n, int s, int e, int ss, int se): name(n), start(s), end(e), s_start(ss), s_end(se), length(0), num_match(0), num_mismatch(0), num_gap(0) {}; const string name; int start; int end; // actual end + 1 int s_start; int s_end; // actual end + 1 int length; int num_match; int num_mismatch; int num_gap; }; /// struct containing annotated gene information struct SIgGene { void Set(const string id, int s, int e) { if (id.substr(0,4) == "lcl|") { sid = id.substr(4, id.size()); } else { sid = id; } start = s; end = e; } void Reset() { sid = ""; start = -1; end = -1; }; string sid; int start; int end; }; /// What delimiter to use between fields in each row of the tabular output. /// Constructor /// @param ostr Stream to write output to [in] /// @param format Output format - what fields to include in the output [in] CIgBlastTabularInfo(CNcbiOstream& ostr, const string& format = kDfltArgTabularOutputFmt, EFieldDelimiter delim = eTab) : CBlastTabularInfo(ostr, format, delim) { }; /// Destructor ~CIgBlastTabularInfo() { x_ResetIgFields(); }; void PrintHeader(const string& program, const objects::CBioseq& bioseq, const string& dbname, const string& domain_sys, const string& rid = kEmptyStr, unsigned int iteration = numeric_limits<unsigned int>::max(), const objects::CSeq_align_set* align_set=0, CConstRef<objects::CBioseq> subj_bioseq = CConstRef<objects::CBioseq>()); /// Set fields for master alignment int SetMasterFields(const objects::CSeq_align& align, objects::CScope& scope, const string& chain_type, const string& master_chain_type_to_show, CNcbiMatrix<int>* matrix=0); /// Set fields for all other alignments int SetFields(const objects::CSeq_align& align, objects::CScope& scope, const string& chain_type, const string& master_chain_type_to_show, CNcbiMatrix<int>* matrix=0); /// Override the print method virtual void Print(void); /// Print domain information void PrintMasterAlign(const string& header = "# ") const; /// Print Html style summary void PrintHtmlSummary() const; /// Set out-of-frame information void SetFrame(const string &frame = "N/A") { m_FrameInfo = frame; }; /// Set strand information void SetMinusStrand(bool minus = true) { m_IsMinusStrand = minus; }; /// Set sequence type void SetSeqType(bool isNucl) { m_IsNucl = isNucl; }; /// Set domain info void AddIgDomain(const string &name, int start, int end, int s_start=-1, int s_end=-1) { if (start <0 || end <= start) return; SIgDomain * domain = new SIgDomain(name, start, end, s_start, s_end); x_ComputeIgDomain(*domain); m_IgDomains.push_back(domain); }; /// Set gene info void SetVGene(const string &id, int s, int e) { m_VGene.Set(id, s,e); } /// Set gene info void SetDGene(const string &id, int s, int e) { m_DGene.Set(id, s,e); } /// Set gene info void SetJGene(const string &id, int s, int e) { m_JGene.Set(id, s,e); } /// One method to set all annotation information void SetIgAnnotation(const CRef<blast::CIgAnnotation> &annot, const CConstRef<blast::CIgBlastOptions> &ig_opts); ///Getter const void GetIgInfo (string& v, string& d, string& j, string& master_chain_to_show, string& cdr3_nuc, string& cdr3_aa, string& productive) const { v = m_VGene.sid; d = m_DGene.sid; j = m_JGene.sid; master_chain_to_show = m_MasterChainTypeToShow; cdr3_nuc = m_Cdr3Seq; cdr3_aa = m_Cdr3SeqTrans; productive = m_OtherInfo[4]; } ///Get Ig domain const vector<SIgDomain*>& GetIgDomains() const { return m_IgDomains; } protected: void x_ResetIgFields(); void x_PrintIgGenes(bool isHtml=false, const string& header="# ") const; void x_ComputeIgDomain(SIgDomain &domain); void x_PrintIgDomain(const SIgDomain &domain) const; void x_PrintIgDomainHtml(const SIgDomain &domain) const; void x_PrintPartialQuery(int start, int end, bool isHtml=false) const; private: string m_Query; bool m_IsNucl; bool m_IsMinusStrand; string m_FrameInfo; string m_ChainType; string m_MasterChainTypeToShow; SIgGene m_VGene; SIgGene m_DGene; SIgGene m_JGene; vector<SIgDomain *> m_IgDomains; // index 4, productive/non-productive // index 3, stop codon or not vector<string> m_OtherInfo; int m_Cdr3Start; int m_Cdr3End; string m_Cdr3Seq; string m_Cdr3SeqTrans; }; END_SCOPE(align_format) END_NCBI_SCOPE #endif /* OBJTOOLS_ALIGN_FORMAT___TABULAR_HPP */

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