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//! [exercise]
#include <array> // std::array
#include <string> // std::string
#include <vector> // std::vector
#include <seqan3/alphabet/all.hpp>
#include <seqan3/argument_parser/all.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/range/views/all.hpp> // optional: use views to convert the input string to a dna5 sequence
using seqan3::operator""_dna5;
int main (int argc, char * argv[])
{
std::string input{};
seqan3::argument_parser parser("GC-Content", argc, argv);
parser.add_positional_option(input, "Specify an input sequence.");
try
{
parser.parse();
}
catch (seqan3::argument_parser_error const & ext) // the input is invalid
{
seqan3::debug_stream << "[PARSER ERROR] " << ext.what() << '\n';
return 0;
}
// Convert the input to a dna5 sequence
std::vector<seqan3::dna5> sequence{};
for (char c : input)
sequence.push_back( seqan3::assign_char_to(c, seqan3::dna5{}) );
// Optional: use views for the conversion. Views will be introduced in the next chapter.
//std::vector<seqan3::dna5> sequence = input | seqan3::views::char_to<seqan3::dna5> | seqan3::views::to<std::vector>;
// Initialise an array with count values for dna5 symbols.
std::array<size_t, seqan3::dna5::alphabet_size> count{}; // default initialised with zeroes
// Increase the symbol count according to the sequence.
for (seqan3::dna5 symbol : sequence)
++count[symbol.to_rank()];
// Calculate the GC content: (#G + #C) / (#A + #T + #G + #C).
size_t gc = count['C'_dna5.to_rank()] + count['G'_dna5.to_rank()];
size_t atgc = input.size() - count['N'_dna5.to_rank()];
float gc_content = 1.0f * gc / atgc;
seqan3::debug_stream << "The GC content of " << sequence << " is " << 100 * gc_content << "%.\n";
return 0;
}
//! [exercise]
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