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//! [alignment]
#include <vector> // for std::vector
#include <tuple> // for std::tie
#include <seqan3/alignment/aligned_sequence/all.hpp> // for alignment stream operator <<
#include <seqan3/alignment/configuration/all.hpp> // for all configs in the seqan3::align_cfg namespace
#include <seqan3/alignment/pairwise/all.hpp> // for seqan3::align_pairwise
#include <seqan3/alphabet/nucleotide/dna5.hpp> // for dna5 datastrucutre
#include <seqan3/argument_parser/all.hpp> // for argument_parser
#include <seqan3/core/debug_stream.hpp> // for debug_stream
#include <seqan3/io/sequence_file/all.hpp> // for sequence_file_input and sequence_file_output
#include <seqan3/std/filesystem> // for tmp_dir
int main()
{
auto tmp_dir = std::filesystem::temp_directory_path();
std::string filename{tmp_dir/"seq.fasta"};
{
// Create a /tmp/my.fasta file.
seqan3::sequence_file_output file_out{filename};
using seqan3::operator""_dna5;
file_out.emplace_back("ACGTGATG"_dna5, std::string{"seq1"});
file_out.emplace_back("AGTGATACT"_dna5, std::string{"seq2"});
}
// Initialise a file input object and a vector
seqan3::sequence_file_input file_in{filename};
std::vector<seqan3::dna5_vector> sequences;
for (auto & [ seq, id, qual ] : file_in)
{
sequences.push_back(seq);
}
// Call a global pairwise alignment with edit distance and traceback.
for (auto && res : align_pairwise(std::tie(sequences[0], sequences[1]),
seqan3::align_cfg::method_global{} |
seqan3::align_cfg::edit_scheme |
seqan3::align_cfg::output_alignment{} |
seqan3::align_cfg::output_score{}))
{
// Print the resulting score and the alignment.
seqan3::debug_stream << res.score() << '\n'; // => -4
seqan3::debug_stream << res.alignment() << '\n'; // => 0 . :
// ACGTGATG--
// | |||||
// A-GTGATACT
}
std::filesystem::remove(filename);
return 0;
}
//! [alignment]
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