com.act.lcms.db.io.report.IonAnalysisInterchangeModelOperations.java Source code

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Here is the source code for com.act.lcms.db.io.report.IonAnalysisInterchangeModelOperations.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.lcms.db.io.report;

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.lang.StringUtils;
import org.apache.commons.lang3.tuple.Pair;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;

public class IonAnalysisInterchangeModelOperations {
    private static final Logger LOGGER = LogManager.getFormatterLogger(IonAnalysisInterchangeModelOperations.class);
    private static final String OPTION_INPUT_FILE = "i";
    private static final String OPTION_OUTPUT_FILE = "o";
    private static final String OPTION_LOG_DISTRIBUTION = "l";

    public static final String HELP_MESSAGE = StringUtils.join(new String[] {
            "This module is used for performing operations on the IonAnalysisInterchangeModelOperations model like computing ",
            "the frequency distribution of intensities or SNR values over molecule hits." }, "");

    public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {
        {
            add(Option.builder(OPTION_INPUT_FILE).argName("input-file")
                    .desc("This option is for taking in an input IonAnalysisInterchangeModel file").hasArg()
                    .longOpt("input-file").required());
            add(Option.builder(OPTION_OUTPUT_FILE).argName("output-file").desc("This option is for the output file")
                    .hasArg().longOpt("output-file").required());
            add(Option.builder(OPTION_LOG_DISTRIBUTION).argName("log-distribution").desc(
                    "This option is for calculating the log distribution of a metric (SNR, Intensity, Time) over molecule"
                            + " counts in the model. One of the metrics needs to be supplied for this analysis to work.")
                    .hasArg().longOpt("log-distribution").required());
        }
    };

    public static final HelpFormatter HELP_FORMATTER = new HelpFormatter();

    static {
        HELP_FORMATTER.setWidth(100);
    }

    public static void main(String[] args) throws IOException {
        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) {
            LOGGER.error("Argument parsing failed: %s", e.getMessage());
            HELP_FORMATTER.printHelp(IonAnalysisInterchangeModelOperations.class.getCanonicalName(), HELP_MESSAGE,
                    opts, null, true);
            System.exit(1);
        }

        if (cl.hasOption("help")) {
            HELP_FORMATTER.printHelp(IonAnalysisInterchangeModelOperations.class.getCanonicalName(), HELP_MESSAGE,
                    opts, null, true);
            System.exit(1);
        }

        if (cl.hasOption(OPTION_LOG_DISTRIBUTION)) {
            IonAnalysisInterchangeModel model = new IonAnalysisInterchangeModel();
            model.loadResultsFromFile(new File(cl.getOptionValue(OPTION_INPUT_FILE)));
            Map<Pair<Double, Double>, Integer> rangeToCount = model
                    .computeLogFrequencyDistributionOfMoleculeCountToMetric(
                            IonAnalysisInterchangeModel.METRIC.valueOf(cl.getOptionValue(OPTION_LOG_DISTRIBUTION)));

            try (BufferedWriter predictionWriter = new BufferedWriter(
                    new FileWriter(new File(OPTION_OUTPUT_FILE)))) {
                for (Map.Entry<Pair<Double, Double>, Integer> entry : rangeToCount.entrySet()) {
                    String value = String.format("%f,%d", entry.getKey().getLeft(), entry.getValue());
                    predictionWriter.write(value);
                    predictionWriter.newLine();
                }
            }
        }
    }
}