unit_test_internal_stops.cpp

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/*  $Id: unit_test_internal_stops.cpp 93111 2021-03-05 15:18:46Z chetvern $
 * ===========================================================================
 *
 *                            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 official 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: Mike DiCuccio
 *
 * File Description:
 *
 * ===========================================================================
 */
 
#include <ncbi_pch.hpp>
 
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbiargs.hpp>
#include <corelib/ncbienv.hpp>
#include <corelib/test_boost.hpp>
 
#include <objmgr/object_manager.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <objmgr/scope.hpp>
 
#include <serial/serial.hpp>
#include <serial/objistr.hpp>
#include <serial/objostr.hpp>
 
#include <algo/sequence/internal_stops.hpp>
 
USING_NCBI_SCOPE;
USING_SCOPE(objects);
 
NCBITEST_INIT_CMDLINE(arg_desc)
{
    // Here we make descriptions of command line parameters that we are
    // going to use.
 
}
 
NCBITEST_AUTO_INIT()
{
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CGBDataLoader::RegisterInObjectManager(*om);
}
 
BOOST_AUTO_TEST_CASE(TestProtein)
{
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CScope scope(*om);
    scope.AddDefaults();
 
string buf = " \
Seq-align ::= { \
  type disc, \
  dim 2, \
  segs spliced { \
    product-id gi 148225248, \
    genomic-id gi 224514980, \
    genomic-strand plus, \
    product-type protein, \
    exons { \
      { \
        product-start protpos { \
          amin 22, \
          frame 1 \
        }, \
        product-end protpos { \
          amin 277, \
          frame 3 \
        }, \
        genomic-start 30641728, \
        genomic-end 30642468, \
        parts { \
          diag 69, \
          product-ins 3, \
          diag 30, \
          product-ins 4, \
          diag 494, \
          product-ins 2, \
          diag 85, \
          product-ins 18, \
          diag 63 \
        }, \
        partial TRUE \
      } \
    }, \
    product-length 278, \
    modifiers { \
      stop-codon-found TRUE \
    } \
  } \
} \
";
 
    CNcbiIstrstream istrs(buf);
 
    unique_ptr<CObjectIStream> istr(CObjectIStream::Open(eSerial_AsnText, istrs));
 
    CSeq_align align;
    *istr >> align;
 
    BOOST_CHECK_NO_THROW(align.Validate(true));
 
    CInternalStopFinder int_stop_finder(scope);
 
    set<TSeqPos> stops = int_stop_finder.FindStops(align);
 
    BOOST_CHECK_EQUAL( stops.size(), 2U );
}
 
/*
BOOST_AUTO_TEST_CASE(TestMRNA)
{
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CScope scope(*om);
    scope.AddDefaults();
 
string buf = " \
Seq-align ::= { \
  type disc, \
  dim 2, \
  segs spliced { \
    product-id gi 178405, \
    genomic-id gi 224514917, \
    product-strand plus, \
    genomic-strand minus, \
    product-type transcript, \
    exons { \
      { \
        product-start nucpos 0, \
        product-end nucpos 2083, \
        genomic-start 78159147, \
        genomic-end 78161233, \
        parts { \
          match 159, \
          genomic-ins 1, \
          match 25, \
          genomic-ins 1, \
          match 47, \
          product-ins 1, \
          match 361, \
          genomic-ins 2, \
          match 1491 \
        } \
      } \
    }, \
    product-length 2084 \
  } \
} \
";
 
    CNcbiIstrstream istrs(buf.c_str());
 
    unique_ptr<CObjectIStream> istr(CObjectIStream::Open(eSerial_AsnText, istrs));
 
    CSeq_align align;
    *istr >> align;
 
    BOOST_CHECK_NO_THROW(align.Validate(true));
 
    CInternalStopFinder int_stop_finder(scope);
 
    set<TSeqPos> stops = int_stop_finder.FindStops(align);
 
    BOOST_CHECK_EQUAL( stops.size(), 9U );
}
*/
 
 
BOOST_AUTO_TEST_CASE(TestStartStopProteinWithPadding)
{
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CScope scope(*om);
    scope.AddDefaults();
 
string buf = " \
Seq-align ::= { \
  type disc, \
  dim 2, \
  segs spliced { \
    product-id gi 148225248, \
    genomic-id gi 224514980, \
    genomic-strand plus, \
    product-type protein, \
    exons { \
      { \
        product-start protpos { \
          amin 22, \
          frame 1 \
        }, \
        product-end protpos { \
          amin 277, \
          frame 3 \
        }, \
        genomic-start 30641728, \
        genomic-end 30642468, \
        parts { \
          diag 69, \
          product-ins 3, \
          diag 30, \
          product-ins 4, \
          diag 494, \
          product-ins 2, \
          diag 85, \
          product-ins 18, \
          diag 63 \
        }, \
        partial TRUE \
      } \
    }, \
    product-length 278, \
    modifiers { \
      stop-codon-found TRUE \
    } \
  } \
} \
";
 
    CNcbiIstrstream istrs(buf);
 
    unique_ptr<CObjectIStream> istr(CObjectIStream::Open(eSerial_AsnText, istrs));
 
    CSeq_align align;
    *istr >> align;
 
    BOOST_CHECK_NO_THROW(align.Validate(true));
 
    CInternalStopFinder int_stop_finder(scope);
 
    pair<set<TSeqPos>, set<TSeqPos> > starts_stops = int_stop_finder.FindStartsStops(align,3);
 
    BOOST_CHECK_EQUAL( starts_stops.first.size(), 10U );
    BOOST_CHECK_EQUAL( starts_stops.second.size(), 3U );
}
 
BOOST_AUTO_TEST_CASE(TestStartAcrossTheOrigin)
{
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CScope scope(*om);
    scope.AddDefaults();
 
string buf = " \
Seq-align ::= { \
  type disc, \
  dim 2, \
  segs spliced { \
    product-id gi 488735231, \
    genomic-id gi 6382081, \
    genomic-strand plus, \
    product-type protein, \
    exons { \
      { \
        product-start protpos { \
          amin 2, \
          frame 3 \
        }, \
        product-end protpos { \
          amin 430, \
          frame 3 \
        }, \
        genomic-start 1, \
        genomic-end 1285, \
        parts { \
          diag 1285 \
        }, \
        partial FALSE \
      } \
    }, \
    product-length 431, \
    modifiers { \
      stop-codon-found TRUE \
    } \
  } \
} \
";
 
    CNcbiIstrstream istrs(buf);
 
    unique_ptr<CObjectIStream> istr(CObjectIStream::Open(eSerial_AsnText, istrs));
 
    CSeq_align align;
    *istr >> align;
 
    BOOST_CHECK_NO_THROW(align.Validate(true));
 
    CInternalStopFinder int_stop_finder(scope);
 
    pair<set<TSeqPos>, set<TSeqPos> > starts_stops = int_stop_finder.FindStartsStops(align,11);
 
    BOOST_CHECK_EQUAL( *starts_stops.first.rbegin(), 30740U );
}
 
BOOST_AUTO_TEST_CASE(TestStopInGap)
{
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CScope scope(*om);
    scope.AddDefaults();
 
string buf = " \
Seq-align ::= { \
  type disc, \
  dim 2, \
  segs spliced { \
    product-id gi 487809918, \
    genomic-id gi 341576043, \
    genomic-strand minus, \
    product-type protein, \
    exons { \
      { \
        product-start protpos { \
          amin 10, \
          frame 1 \
        }, \
        product-end protpos { \
          amin 165, \
          frame 3 \
        }, \
        genomic-start 84235, \
        genomic-end 84618, \
        parts { \
          diag 6, \
          genomic-ins 6, \
          diag 48, \
          product-ins 3, \
          diag 12, \
          product-ins 15, \
          diag 18, \
          product-ins 72, \
          diag 294 \
        }, \
        partial TRUE \
      } \
    }, \
    product-length 166, \
    modifiers { \
      start-codon-found TRUE, \
      stop-codon-found TRUE \
    } \
  } \
} \
";
 
    CNcbiIstrstream istrs(buf);
 
    unique_ptr<CObjectIStream> istr(CObjectIStream::Open(eSerial_AsnText, istrs));
 
    CSeq_align align;
    *istr >> align;
 
    BOOST_CHECK_NO_THROW(align.Validate(true));
 
    CInternalStopFinder int_stop_finder(scope);
 
    CFeatureGenerator fg(scope);
    fg.SetFlags(CFeatureGenerator::fMaximizeTranslation);
    CConstRef<CSeq_align> clean_alignment = fg.CleanAlignment(align);
    set<TSeqPos> stops = int_stop_finder.FindStops(*clean_alignment);
 
    BOOST_CHECK_EQUAL( *stops.begin(), 84609U );
}
 
BOOST_AUTO_TEST_CASE(TestAltStarts)
{
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CScope scope(*om);
    scope.AddDefaults();
 
string buf = " \
Seq-align ::= { \
  type disc, \
  dim 2, \
  segs spliced { \
    product-id gi 148225248, \
    genomic-id gi 224514980, \
    genomic-strand plus, \
    product-type protein, \
    exons { \
      { \
        product-start protpos { \
          amin 22, \
          frame 1 \
        }, \
        product-end protpos { \
          amin 277, \
          frame 3 \
        }, \
        genomic-start 30641728, \
        genomic-end 30642468, \
        parts { \
          diag 69, \
          product-ins 3, \
          diag 30, \
          product-ins 4, \
          diag 494, \
          product-ins 2, \
          diag 85, \
          product-ins 18, \
          diag 63 \
        }, \
        partial TRUE \
      } \
    }, \
    product-length 278, \
    modifiers { \
      stop-codon-found TRUE \
    } \
  } \
} \
";
 
    CNcbiIstrstream istrs(buf);
 
    unique_ptr<CObjectIStream> istr(CObjectIStream::Open(eSerial_AsnText, istrs));
 
    CSeq_align align;
    *istr >> align;
 
    BOOST_CHECK_NO_THROW(align.Validate(true));
 
    CInternalStopFinder int_stop_finder(scope);
 
    typedef map<TSeqRange, string> TStarts;
    TStarts starts = int_stop_finder.FindStartStopRanges(align,3).first;
 
    int atg_starts = 0;
    ITERATE(TStarts, s, starts) {
        if (s->second == "ATG")
            ++atg_starts;
    }
 
    BOOST_CHECK_EQUAL( atg_starts, 3 );
}
 
BOOST_AUTO_TEST_CASE(TestAtCircularEnd)
{
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CScope scope(*om);
    scope.AddDefaults();
 
string buf = " \
Seq-align ::= { \
  type disc, \
  dim 2, \
  segs spliced { \
    product-id gi 490246827, \
    genomic-id gi 364515570, \
    genomic-strand minus, \
    product-type protein, \
    exons { \
      { \
        product-start protpos { \
          amin 0, \
          frame 1 \
        }, \
        product-end protpos { \
          amin 628, \
          frame 3 \
        }, \
        genomic-start 5332055, \
        genomic-end 5333941, \
        parts { \
          match 3, \
          diag 1884 \
        } \
      } \
    }, \
    product-length 629, \
    modifiers { \
      start-codon-found TRUE, \
      stop-codon-found TRUE \
    } \
  } \
} \
";
 
    CNcbiIstrstream istrs(buf);
 
    unique_ptr<CObjectIStream> istr(CObjectIStream::Open(eSerial_AsnText, istrs));
 
    CSeq_align align;
    *istr >> align;
 
    BOOST_CHECK_NO_THROW(align.Validate(true));
 
    CInternalStopFinder int_stop_finder(scope);
 
    for (int pad=33; pad > 30; --pad) {
        auto starts_stops_ranges = int_stop_finder.FindStartStopRanges(align, pad);
 
        BOOST_CHECK( starts_stops_ranges.first.find(TSeqRange(5333941,5333939)) != starts_stops_ranges.first.end() );
        BOOST_CHECK_EQUAL( starts_stops_ranges.first[TSeqRange(5333941,5333939)], "ATG" );
    }
}
 
BOOST_AUTO_TEST_CASE(TestReportGaps)
{
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CScope scope(*om);
    scope.AddDefaults();
 
string buf = " \
Seq-align ::= { \
  type disc, \
  dim 2, \
  segs spliced { \
    product-id gi 487427171, \
    genomic-id gi 357958168, \
    genomic-strand plus, \
    product-type protein, \
    exons { \
      { \
        product-start protpos { \
          amin 3, \
          frame 1 \
        }, \
        product-end protpos { \
          amin 96, \
          frame 3 \
        }, \
        genomic-start 31, \
        genomic-end 312, \
        parts { \
          diag 282 \
        }, \
        partial TRUE \
      } \
    }, \
    product-length 97 \
  } \
} \
";
 
    CNcbiIstrstream istrs(buf);
 
    unique_ptr<CObjectIStream> istr(CObjectIStream::Open(eSerial_AsnText, istrs));
 
    CSeq_align align;
    *istr >> align;
 
    BOOST_CHECK_NO_THROW(align.Validate(true));
 
    CInternalStopFinder int_stop_finder(scope);
 
    set<TSignedSeqRange> gaps;
    auto starts_stops = int_stop_finder.FindStartStopRanges(align, 1100, &gaps);
 
    BOOST_CHECK_EQUAL( gaps.size(), 3U );
    auto it = gaps.begin();
    BOOST_CHECK_EQUAL( it->GetFrom(), -10 );
    BOOST_CHECK_EQUAL( it->GetTo(),   -1 );
    ++it;
    BOOST_CHECK_EQUAL( it->GetFrom(), 26 );
    BOOST_CHECK_EQUAL( it->GetTo(),   28 );
    ++it;
    BOOST_CHECK_EQUAL( it->GetFrom(), 1405 );
    BOOST_CHECK_EQUAL( it->GetTo(),   1414 );
}