Extract lists of pquery names per branch of the reference tree, using genesis v0.7.0 (https://github.com/lczech/genesis).

extract_branch_placements.cpp

/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2016 Lucas Czech

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.

    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/

#include <assert.h>
#include <stdexcept>
#include <string>
#include <unordered_map>
#include <utility>
#include <vector>

#include "placement/function/functions.hpp"
#include "placement/formats/jplace_reader.hpp"
#include "placement/sample.hpp"

#include "utils/core/logging.hpp"
#include "utils/core/fs.hpp"
#include "utils/text/string.hpp"

using namespace genesis;

// =================================================================================================
//     Main Function
// =================================================================================================

int main( int argc, char** argv )
{
    using namespace ::genesis::placement;

    // Activate logging.
    utils::Logging::log_to_stdout();

    // Check if the command line contains the right number of arguments and store them.
    if (argc != 3) {
        throw std::runtime_error(
            "Need to provide two command line arguments:\n"
            "  * An input jplace file path.\n"
            "  * An output directory path."
        );
    }
    auto jplace_filename = std::string( argv[1] );
    auto output_dir      = utils::trim_right( std::string( argv[2] ), "/") + "/";

    // Some user output.
    LOG_INFO << "Using jplace file      " << jplace_filename;
    LOG_INFO << "Using outout directory " << output_dir;

    // Read the Jplace file into a Sample object.
    Sample sample;
    JplaceReader().from_file( jplace_filename, sample );

    // Some more output.
    LOG_INFO << "Found " << sample.pquery_size() << " pqueries in sample.";

    // Remove all but the most likely placement position for each pquery.
    placement::filter_n_max_weight_placements( sample, 1 );

    // Create a list of pquery names per edge of the tree, indexed by the edge index.
    std::unordered_map< size_t, std::string > edge_pquery_names;
    for( auto const& pqry : sample.pqueries() ) {

        // We can be sure that there is at most one placement for the pquery, as we just filtered
        // out all others. If there is none, this is an empty pquery, so issue a warning and skip it.
        assert( pqry.placement_size() <= 1 );
        if( pqry.placement_size() == 0 ) {
            LOG_WARN << "Pquery without any placements found. Skipping this.";
            continue;
        }

        // Skip if there is no name (this pquery cannot be identified anyway, so there is no need
        // to add a default name to the list).
        if( pqry.name_size() == 0 ) {
            LOG_WARN << "Pquery without name found. Skipping this.";
            continue;
        }

        // Add the first name of the pquery to the list at the according edge index.
        auto const& placement = pqry.placement_at( 0 );
        edge_pquery_names[ placement.edge().index() ] += pqry.name_at( 0 ).name + "\n";
    }

    // Now write out all edge index lists to the output dir.
    for( auto const& edge_output : edge_pquery_names ) {
        auto filename = output_dir + "edge_" + utils::to_string( edge_output.first ) + ".txt";

        // Skip if file exists.
        if( utils::file_exists( filename )) {
            LOG_WARN << "Output file " << filename << " exists. Skipping.";
            continue;
        }

        utils::file_write( edge_output.second, filename );
    }

    LOG_INFO << "Finished.";
    return 0;
}