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alignment_file_solution2.cpp
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alignment_file_solution2.cpp
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#include <fstream>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/std/filesystem>
struct write_file_dummy_struct
{
std::filesystem::path const tmp_path = std::filesystem::temp_directory_path();
write_file_dummy_struct()
{
auto fasta_file_raw = R"////![ref_file]";
auto file_raw = R"////![sam_file]";
std::ofstream file{tmp_path/"mapping.sam"};
std::string str{file_raw};
file << str.substr(1); // skip first newline
std::ofstream reffile{tmp_path/"reference.fasta"};
std::string fasta_file_rawstr{fasta_file_raw};
reffile << fasta_file_rawstr.substr(1); // skip first newline
}
~write_file_dummy_struct()
{
std::error_code ec{};
std::filesystem::path file_path{};
file_path = tmp_path/"mapping.sam";
std::filesystem::remove(file_path, ec);
if (ec)
seqan3::debug_stream << "[WARNING] Could not delete " << file_path << ". " << ec.message() << '\n';
file_path = tmp_path/"reference.fasta";
std::filesystem::remove(file_path, ec);
if (ec)
seqan3::debug_stream << "[WARNING] Could not delete " << file_path << ". " << ec.message() << '\n';
}
};
write_file_dummy_struct go{};
//![solution]
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/io/alignment_file/all.hpp>
#include <seqan3/io/sequence_file/all.hpp>
#include <seqan3/alphabet/gap/gap.hpp>
#include <seqan3/std/filesystem>
#include <seqan3/std/ranges>
using namespace seqan3;
struct my_traits : public sequence_file_input_default_traits_dna
{
//!\brief The container for sequences is now std::vector seqan3::concatenated_sequences.
template <typename _sequence_container>
using sequence_container_container = std::vector<_sequence_container>;
};
int main()
{
std::filesystem::path tmp_dir = std::filesystem::temp_directory_path(); // get the temp directory
// read in reference information
sequence_file_input<my_traits> reference_file{tmp_dir/"reference.fasta"};
concatenated_sequences<std::string> ref_ids = get<field::ID>(reference_file);
std::vector<std::vector<dna5>> ref_seqs = get<field::SEQ>(reference_file);
alignment_file_input mapping_file{tmp_dir/"mapping.sam",
ref_ids,
ref_seqs,
fields<field::ID,field::REF_ID, field::MAPQ, field::ALIGNMENT>{}};
auto mapq_filter = std::views::filter([] (auto & rec) { return get<field::MAPQ>(rec) >= 30; });
for (auto & [id, ref_id, mapq, alignment] : mapping_file | mapq_filter)
{
auto & ref = get<0>(alignment);
size_t sum_ref{};
std::ranges::for_each(ref.begin(), ref.end(), [&sum_ref] (auto c) { if (c == gap{}) ++sum_ref; });
auto & read = get<0>(alignment);
size_t sum_read{};
std::ranges::for_each(read.begin(), read.end(), [&sum_read] (auto c) { if (c == gap{}) ++sum_read; });
debug_stream << id << " mapped against " << ref_id << " with "
<< sum_read << " gaps in the read sequence and "
<< sum_ref << " gaps in the reference sequence." << std::endl;
}
}
//![solution]