1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
|
#include <seqan3/alphabet/nucleotide/dna4.hpp> // to create right datastructure in tmp file
#include <seqan3/io/sequence_file/output.hpp> // to create tmp file
#include <seqan3/std/filesystem> // to create tmp directory
// This creates a temporary file to ensure that the snippet works correctly without any dependency on external files.
struct write_file_dummy_struct
{
std::filesystem::path const file_path = std::filesystem::temp_directory_path()/"seq.fasta";
write_file_dummy_struct()
{
auto file_raw = R"////![fasta_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{};
//! [fileinput]
#include <string>
#include <seqan3/core/debug_stream.hpp> // for debug_stream
#include <seqan3/io/sequence_file/input.hpp> // for sequence_file_input
int main ()
{
std::filesystem::path tmp_dir = std::filesystem::temp_directory_path(); // get the tmp directory
// Initialise a file input object with a FastA file.
seqan3::sequence_file_input file_in{tmp_dir/"seq.fasta"};
// Retrieve the sequences and ids.
for (auto & [seq, id, qual] : file_in)
{
seqan3::debug_stream << "ID: " << id << '\n';
seqan3::debug_stream << "SEQ: " << seq << '\n';
seqan3::debug_stream << "Empty Qual." << qual << '\n'; // qual is empty for FastAfiles
}
return 0;
}
//! [fileinput]
|
