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NCBI C++ ToolKit: CAlignFilter Class Reference

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CAlignFilter exposes a query language for inspecting properties and scores placed on Seq-align objects. More...

#include <algo/align/util/align_filter.hpp>

CAlignFilter exposes a query language for inspecting properties and scores placed on Seq-align objects.

The query language supports a wide variety of parameters and language structures.

Basic syntax ------------

• Queries can contain any mix of balanced parentheses
• Queries can use standard boolean operators (AND / OR / NOT; operators are not case sensitive)
• Queries consist of tokens expressing a conditional phrase, of the forms:
  1. a = b
  2. a != b
  3. a < b
  4. a > b
• Tokens may be a numeric or a text string. Text strings are evaluated in a dictionary against a list of known computable values. If a text string is not found in the computed dictionary, the text string is looked up as a score in Seq-align.score.
• CAlignFilter supports a set of functions as well. Functions express additional parameters or mathematical operations. The current list of functions is:
  1. MUL(a, b) = a * b; a and b are tokens as defined above
  2. ADD(a, b) = a + b; a and b are tokens as defined above
  3. IS_SEG_TYPE(a) = 1 if the Seq-align is of segment type a (where a is one of 'disc', 'denseg', 'std', 'spliced', 'packed', 'dendiag')
  4. COALESCE(a,b,...) = first of (a, b, ...) that evaluates to a supported value. In order to avoid problems when querying against a missing value, COALESCE() allows the specification of alternate score names or of alternate values. Thus, COALESCE(score, 0) will return 0 if 'score' is not present.

Current Accepted Tokens -----------------------

• Any named score. CSeq_align enforces through the use of enums specific score names; some standard score names are described in CSeq_align and include:
  1. align_length
  2. bit_score
  3. comp_adjustment_method
  4. e_value
  5. longest_gap
  6. num_ident
  7. num_mismatch
  8. num_negatives
  9. num_positives
  10. pct_coverage
  11. pct_identity_gap
  12. pct_identity_gapopen_only
  13. pct_identity_ungap
  14. score
  15. sum_e NOTE: There is no requirement that an alignment contain any of the above scores.
• Any number. All numbers are interpreted as doubles.
• One of a fixed set of computable characteristics locally defined in CAlignFilter. These include:
  1. 3prime_unaligned - Length of 3' unaligned sequence
  2. 5prime_unaligned - Length of 5' unaligned sequence (same as query_start)
  3. align_length - Length of aligned query span
  4. align_length_ratio - Length of aligned subject span / length of aligned query span
  5. align_length_ungap - Sum of lengths of aligned query segments
  6. cds_internal_stops - For Spliced-segs, returns the count of the number of internal stops present in the mapped CDS (mapped = CGeneModel::CreateGeneModel() mapped)
  7. internal_unaligned - Length of unaligned sequence between 5'-most and 3'-most ends
  8. min_exon_len - Length of shortest exon
  9. product_length - Same as query_length
  10. query_end - End pos (0-based) of query sequence
  11. query_length - Length of query sequence
  12. query_start - Start pos (0-based) of query sequence
  13. subject_end - Ending pos (0-based) of subject span
  14. subject_length - Length of subject length
  15. subject_start - Starting pos (0-based) of subject span
• A specific sequence identifier. The special tokens 'query' and 'subject' can be used to specify individual sequences using any of the sequence's seq-id synonyms

Example queries: ----------------

• pct_coverage > 99.5
  • finds alignments with the score pct_coverage > 99.5
• (pct_identity_gap > 99.9 AND pct_coverage > 98) OR (pct_identity_gap > 99.0 AND pct_coverage > 99.5)
  • Evaluates two simultaneous logical conditions, returning the inclusive OR set
• query = NM_012345.1
  • returns all alignments for the query sequence
• MUL(align_length, 0.8) > num_positives
  • evaluates for all alignments for which num_positives covers 80% of the aligned length

Definition at line 158 of file align_filter.hpp.

Range restriction infrastructure For some query/subject pairs, we will restrict the alignments to lie within a specified range.

Definition at line 293 of file align_filter.hpp.

Add a sequence to a blacklist.

Blacklisted sequences are excluded always; if an alignment contains a query or subject that matches a blacklisted alignment, then that alignment will be excluded.

NOTE: this is only triggered if the alignments are pairwise!

Definition at line 215 of file align_filter.cpp.

References set< Key, Compare >::insert(), and m_QueryBlacklist.

Filter a set of alignments, iteratively applying Match() to each alignment and emitting all matched alignments in the output set.

Filter a set of alignments, iteratively applying Match() to each alignment and emitting all matched alignments in the output seq-annot.

Match a single alignment.

Definition at line 310 of file align_filter.cpp.

References CSeq_align::CheckNumRows(), eGetId_Canonical, map_checker< Container >::empty(), map_checker< Container >::end(), set< Key, Compare >::end(), map_checker< Container >::find(), set< Key, Compare >::find(), CSeq_id_Handle::GetHandle(), GetId(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqRange(), COpenRange< Position >::IntersectingWith(), m_ParseTree, m_QSComparts, m_QueryBlacklist, m_QueryExcludeNotIn, m_QueryWhitelist, m_RemoveDuplicates, m_Scope, m_ScoreLookup, m_SubjectBlacklist, m_SubjectExcludeNotIn, m_SubjectWhitelist, match(), query, r(), set< Key, Compare >::size(), subject, x_IsUnique(), and x_Match().

Referenced by BOOST_AUTO_TEST_CASE(), CAlignSort::MergeSortedFiles(), s_GetCDSLoc(), and CAlignSort::SortAlignments().

Set the query to be used.

Definition at line 159 of file align_filter.cpp.

References DryRun(), CQueryParseTree::eCaseInsensitive, CQueryParseTree::eSyntaxCheck, CObjectManager::GetInstance(), m_ParseTree, m_Query, m_Scope, NULL, CRef< C, Locker >::Reset(), and x_ParseTree_Flatten().

Referenced by CAlignFilter().

Definition at line 517 of file align_filter.cpp.

References CSeqdesc_Base::e_Embl, CSeqdesc_Base::e_Genbank, CSeqdesc_Base::e_Pir, CSeqdesc_Base::e_Prf, CSeqdesc_Base::e_Sp, eGetId_Best, CRangeCollection< Position >::Empty(), NStr::EqualNocase(), CQueryParseNode::eString, eUnknown, map_checker< Container >::find(), CSeq_align::GetAlignedBases(), CSeq_id_Handle::GetHandle(), GetId(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CTreeNode< TValue, TKeyGetterP >::GetValue(), CRangeCollection< Position >::IntersectWith(), CSeq_align_Base::C_Segs::IsDendiag(), CSeq_align_Base::C_Segs::IsDenseg(), CSeq_align_Base::C_Segs::IsDisc(), CSeq_align_Base::C_Segs::IsPacked(), CSeq_align_Base::C_Segs::IsSparse(), CSeq_align_Base::C_Segs::IsSpliced(), CSeq_align_Base::C_Segs::IsStd(), ITERATE, m_IsDryRun, m_Scope, NCBI_THROW, NULL, NStr::NumericToString(), round(), row, CTreeNode< TValue, TKeyGetterP >::SubNodeBegin(), CTreeNode< TValue, TKeyGetterP >::SubNodeEnd(), v2, x_GetRegionMap(), and x_TermValue().

Referenced by x_TermValue().

Definition at line 881 of file align_filter.cpp.

References CFormatGuess::eBinaryASN, map_checker< Container >::empty(), eSerial_AsnBinary, eSerial_AsnText, CFormatGuess::eTextASN, eUnknown, format, CSeq_annot_Base::GetData(), CSeq_annot_Base::C_Data::GetFtable(), CSeq_id_Handle::GetHandle(), CFormatGuess::GuessFormat(), CSeq_annot::IsFtable(), m_RegionMapCache, NCBI_THROW, NStr::NumericToString(), and CObjectIStream::Open().

Referenced by x_FuncCall().

Definition at line 1238 of file align_filter.cpp.

References CQueryParseNode::eAnd, CQueryParseNode::eBetween, CQueryParseNode::eEQ, CQueryParseNode::eGE, CQueryParseNode::eGT, CQueryParseNode::eLE, CQueryParseNode::eLT, CQueryParseNode::eNot, CQueryParseNode::eOr, CQueryParseNode::eString, eUnknown, CTreeNode< TValue, TKeyGetterP >::GetValue(), m_IsDryRun, NCBI_THROW, CTreeNode< TValue, TKeyGetterP >::SubNodeBegin(), CTreeNode< TValue, TKeyGetterP >::SubNodeEnd(), x_Query_Op(), x_Query_Range(), and x_TermValue().

Referenced by DryRun(), and Match().

Definition at line 74 of file align_filter.cpp.

References CTreeNode< TValue, TKeyGetterP >::AddNode(), CTreeNode< TValue, TKeyGetterP >::DetachNode(), CQueryParseNode::eAnd, CScoreLookup::IScore::eEasy, CScoreLookup::IScore::eHard, CQueryParseNode::eOr, ITERATE, CTreeNode< TValue, TKeyGetterP >::RemoveNode(), CTreeNode< TValue, TKeyGetterP >::SubNodeBegin(), CTreeNode< TValue, TKeyGetterP >::SubNodeEnd(), and x_Complexity().

Referenced by SetFilter().

Definition at line 966 of file align_filter.cpp.

References CSeq_id_Handle::AsString(), CSeqdesc_Base::e_User, CQueryParseNode::eEQ, CQueryParseNode::eGE, eGetId_Best, CQueryParseNode::eGT, CQueryParseNode::eLE, CQueryParseNode::eLT, eNa_strand_both, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, NStr::EqualNocase(), ERR_POST, CQueryParseNode::eString, eUnknown, CUser_field_Base::GetData(), CUser_object::GetField(), CSeq_id_Handle::GetHandle(), GetId(), CSeq_align::GetSeq_id(), CSynonymsSet::GetSeq_id_Handle(), CSeq_id_Handle::GetSeqId(), CSeq_align::GetSeqStrand(), CObject_id_Base::GetStr(), CUser_field_Base::C_Data::GetStr(), CUser_object_Base::GetType(), CTreeNode< TValue, TKeyGetterP >::GetValue(), isnan, CSeq_id_Base::IsOther(), CObject_id_Base::IsStr(), ITERATE, m_IsDryRun, m_Scope, NCBI_ASSERT, NCBI_THROW, val, Warning(), and x_TermValue().

Referenced by x_Match().

Definition at line 931 of file align_filter.cpp.

References CQueryParseNode::eFloatConst, CQueryParseNode::eFunction, CQueryParseNode::eIntConst, CQueryParseNode::eString, eUnknown, CTreeNode< TValue, TKeyGetterP >::GetValue(), NCBI_THROW, s_IsDouble(), str(), NStr::StringToDouble(), val, x_FuncCall(), and x_GetAlignmentScore().

Referenced by x_FuncCall(), x_Match(), x_Query_Op(), and x_Query_Range().

The documentation for this class was generated from the following files:

• include/algo/align/util/align_filter.hpp
• src/algo/align/util/align_filter.cpp

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