com.act.biointerpretation.cofactorremoval.ReactionCofactorRemover.java Source code

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Here is the source code for com.act.biointerpretation.cofactorremoval.ReactionCofactorRemover.java

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/*************************************************************************
*                                                                        *
*  This file is part of the 20n/act project.                             *
*  20n/act enables DNA prediction for synthetic biology/bioengineering.  *
*  Copyright (C) 2017 20n Labs, Inc.                                     *
*                                                                        *
*  Please direct all queries to act@20n.com.                             *
*                                                                        *
*  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/>. *
*                                                                        *
*************************************************************************/

package com.act.biointerpretation.cofactorremoval;

import act.server.NoSQLAPI;
import act.shared.Reaction;
import com.act.biointerpretation.desalting.ReactionDesalter;
import com.act.lcms.db.io.LoadPlateCompositionIntoDB;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.CommandLineParser;
import org.apache.commons.cli.DefaultParser;
import org.apache.commons.cli.HelpFormatter;
import org.apache.commons.cli.Option;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

import java.util.ArrayList;
import java.util.List;

public class ReactionCofactorRemover {
    private static final Logger LOGGER = LogManager.getFormatterLogger(ReactionCofactorRemover.class);

    public static final String OPTION_READ_DB = "d";
    public static final String OPTION_RXN_ID = "r";
    public static final String HELP_MESSAGE = StringUtils.join(
            new String[] { "This class removes cofactors from a single reaction and prints the results to stdout. ",
                    "To remove cofactors from an entire installer DB, use BiointerpretationDriver." },
            "");

    public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {
        {
            add(Option.builder(OPTION_READ_DB).argName("read db name").desc("The name of the read DB to use")
                    .hasArg().required().longOpt("db"));
            add(Option.builder(OPTION_RXN_ID).argName("id")
                    .desc("The id of the reaction from which to remove cofactors").hasArg().required()
                    .longOpt("id"));
            add(Option.builder("h").argName("help").desc("Prints this help message").longOpt("help"));
        }
    };
    public static final HelpFormatter HELP_FORMATTER = new HelpFormatter();

    static {
        HELP_FORMATTER.setWidth(100);
    }

    public static void main(String[] args) throws Exception {
        Options opts = new Options();
        for (Option.Builder b : OPTION_BUILDERS) {
            opts.addOption(b.build());
        }

        CommandLine cl = null;
        try {
            CommandLineParser parser = new DefaultParser();
            cl = parser.parse(opts, args);
        } catch (ParseException e) {
            System.err.format("Argument parsing failed: %s\n", e.getMessage());
            HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null,
                    true);
            System.exit(1);
        }

        if (cl.hasOption("help")) {
            HELP_FORMATTER.printHelp(ReactionDesalter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
            return;
        }

        NoSQLAPI api = new NoSQLAPI(cl.getOptionValue(OPTION_READ_DB), cl.getOptionValue(OPTION_READ_DB));

        CofactorRemover cofactorRemover = new CofactorRemover(api);
        cofactorRemover.init();

        Pair<Reaction, Reaction> results = cofactorRemover
                .removeCofactorsFromOneReaction(Long.parseLong(cl.getOptionValue(OPTION_RXN_ID)));

        System.out.format("Reaction before processing:\n");
        printReport(results.getLeft());
        System.out.println();
        System.out.format("Reaction after processing:\n");
        printReport(results.getRight());
        System.out.println();
    }

    private static void printReport(Reaction rxn) {
        System.out.format("Reaction before processing:\n");
        System.out.format("  Substrates:      %s\n", StringUtils.join(rxn.getSubstrates(), ", "));
        System.out.format("  Products:        %s\n", StringUtils.join(rxn.getProducts(), ", "));
        System.out.format("  Sub. cofactors:  %s\n", StringUtils.join(rxn.getSubstrateCofactors(), ", "));
        System.out.format("  Prod. cofactors: %s\n", StringUtils.join(rxn.getProductCofactors(), ", "));
        System.out.format("  Coenzymes:       %s\n", StringUtils.join(rxn.getCoenzymes(), ", "));
    }
}