FastaOperations.cc

//\file FastaOperations.cc

#include <Sequence/Fasta.hpp>
#include <string>
#include <iostream>
#include <algorithm>
#include <numeric>
#include <boost/test/unit_test.hpp>

struct fasta_operations_fixture
{
    std::string name, seq;
    fasta_operations_fixture()
        : name{ "seqname" }, seq{ "AGCGTAGACAGTAGAGTGAT" }
    {
    }
};

BOOST_FIXTURE_TEST_SUITE(FastaOperationsTest, fasta_operations_fixture)

//A generic revcom routine written for this test
std::string rcom( const std::string & s )
{
  std::string rv(s);
  std::reverse(rv.begin(),rv.end());
  std::transform(rv.begin(),rv.end(),
                 rv.begin(),
                 [](const char & ch)
                 {
                   switch(ch)
                     {
                     case 'A':
                       return 'T';
                       break;
                     case 'G':
                       return 'C';
                       break;
                     case 'C':
                       return 'G';
                       break;
                     case 'T':
                       return 'A';
                       break;
                     }
                   return 'N';
                 });
  return rv;
}


BOOST_AUTO_TEST_CASE( revcom )
{
  std::string name("seqname"),seq("AGCGTAGACAGTAGAGTGAT");
  Sequence::Fasta f(name,seq);

  Sequence::Fasta f2 = f;
  f2.Revcom();

  BOOST_REQUIRE( f2.seq == rcom(seq) );
}

BOOST_AUTO_TEST_CASE( subseq )
{
  std::string name("seqname"),seq("AGCGTAGACAGTAGAGTGAT");
  Sequence::Fasta f(name,seq);

  Sequence::Fasta f3(f);
  f3.Subseq(1,3);

  BOOST_REQUIRE( f3.seq == "GCG" );

  f3.Complement();

  BOOST_REQUIRE( f3.seq == "CGC" );

  BOOST_REQUIRE( std::string(f3) == "CGC" ); //operator string()

}


BOOST_AUTO_TEST_CASE( gapped )
{
  Sequence::Fasta f3("seqname","GCG");

  BOOST_REQUIRE( !f3.IsGapped() );

  f3.seq += '-';

  BOOST_REQUIRE( f3.IsGapped() );

  BOOST_REQUIRE( f3.length() == 4 );

  BOOST_REQUIRE( f3.UngappedLength() == 3 );

  //Remove the gap
  f3.seq.erase( f3.seq.find('-'), 1 );

  BOOST_REQUIRE( f3.length() == 3 );

  BOOST_REQUIRE( f3.UngappedLength() == 3 );
}

BOOST_AUTO_TEST_CASE( cpp11access_1 )
{
  Sequence::Fasta f3("seqname","GCG");
  for( auto & d  : f3 )
    {
      d = 'A';
    }
  BOOST_REQUIRE_EQUAL(f3.seq,"AAA");
}

BOOST_AUTO_TEST_SUITE_END()
//EOF