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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 file_path = std::filesystem::temp_directory_path()/"my.fastq";
write_file_dummy_struct()
{
auto file_raw = R"////![fastq_file]";
std::ofstream file{file_path};
std::string str{file_raw};
file << str.substr(1); // skip first newline
}
~write_file_dummy_struct()
{
std::error_code ec{};
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/sequence_file/all.hpp>
#include <seqan3/range/views/get.hpp>
#include <seqan3/range/views/move.hpp>
#include <seqan3/std/filesystem>
#include <seqan3/std/ranges>
int main()
{
#if !SEQAN3_WORKAROUND_GCC_96070
std::filesystem::path tmp_dir = std::filesystem::temp_directory_path(); // get the temp directory
seqan3::sequence_file_input fin{tmp_dir/"my.fastq"};
auto length_filter = std::views::filter([] (auto const & rec)
{
return std::ranges::size(seqan3::get<seqan3::field::seq>(rec)) >= 5;
});
// you can use a for loop
// for (auto & rec : fin | length_filter | std::views::take(2))
// {
// seqan3::debug_stream << "ID: " << seqan3::get<seqan3::field::id>(rec) << '\n';
// }
// But you can also do this to retrieve all IDs into a vector:
std::vector<std::string> ids = fin
| length_filter // apply length filter
| std::views::take(2) // take first two records
| seqan3::views::get<seqan3::field::id> // select only ID from record
| seqan3::views::move // mark ID to be moved out of record
| seqan3::views::to<std::vector<std::string>>; // convert to container
// Note that you need to know the type of id (std::string)
seqan3::debug_stream << ids << '\n';
#endif // !SEQAN3_WORKAROUND_GCC_96070
}
//![solution]
|
