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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 <string>
#include <vector>
#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/gap/gap.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/io/alignment_file/input.hpp>
#include <seqan3/io/record.hpp>
#include <seqan3/io/sequence_file/input.hpp>
#include <seqan3/std/filesystem>
#include <seqan3/std/ranges>
int main()
{
std::filesystem::path tmp_dir = std::filesystem::temp_directory_path(); // get the temp directory
// read in reference information
seqan3::sequence_file_input reference_file{tmp_dir/"reference.fasta"};
std::vector<std::string> ref_ids{};
std::vector<seqan3::dna5_vector> ref_seqs{};
for (auto && record : reference_file)
{
ref_ids.push_back(std::move(seqan3::get<seqan3::field::id>(record)));
ref_seqs.push_back(std::move(seqan3::get<seqan3::field::seq>(record)));
}
using field_type = seqan3::fields<seqan3::field::id,
seqan3::field::ref_id,
seqan3::field::mapq,
seqan3::field::alignment>;
seqan3::alignment_file_input mapping_file{tmp_dir/"mapping.sam", ref_ids, ref_seqs, field_type{}};
#if !SEQAN3_WORKAROUND_GCC_93983
auto mapq_filter = std::views::filter([] (auto & rec) { return seqan3::get<seqan3::field::mapq>(rec) >= 30; });
#endif // !SEQAN3_WORKAROUND_GCC_93983
#if SEQAN3_WORKAROUND_GCC_93983
for (auto & [id, ref_id, mapq, alignment] : mapping_file /*| mapq_filter*/)
#else // ^^^ workaround / no workaround vvv
for (auto & [id, ref_id, mapq, alignment] : mapping_file | mapq_filter)
#endif // SEQAN3_WORKAROUND_GCC_93983
{
using seqan3::get;
size_t sum_ref{};
for (auto const & char_ref : get<0>(alignment))
if (char_ref == seqan3::gap{})
++sum_ref;
size_t sum_read{};
for (auto const & char_read : get<1>(alignment))
if (char_read == seqan3::gap{})
++sum_read;
seqan3::debug_stream << id << " mapped against " << ref_id << " with "
<< sum_read << " gaps in the read sequence and "
<< sum_ref << " gaps in the reference sequence.\n";
}
}
//![solution]
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