com.act.biointerpretation.l2expansion.L2PredictionCorpusOperations.java Source code

Introduction

Here is the source code for com.act.biointerpretation.l2expansion.L2PredictionCorpusOperations.java

Source

/*************************************************************************
*                                                                        *
*  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.l2expansion;

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.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;

import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

public class L2PredictionCorpusOperations {
    private static final Logger LOGGER = LogManager.getFormatterLogger(L2PredictionCorpusOperations.class);
    private static final String OPTION_WRITE_PRODUCTS_AS_LIST_OF_INCHIS = "f";
    private static final String OPTION_INPUT_PATH = "i";

    public static final String HELP_MESSAGE = StringUtils.join(new String[] {
            "This module is used to perform operations on L2PredictionCorpus results, like getting products from the all ",
            "substrates of the model" }, "");

    public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {
        {
            add(Option.builder(OPTION_INPUT_PATH).argName("input file path")
                    .desc("The input path of the prediction corpus").hasArg().longOpt("input-file-path")
                    .required(true));
            add(Option.builder(OPTION_WRITE_PRODUCTS_AS_LIST_OF_INCHIS)
                    .argName("get list of products from prediction corpus")
                    .desc("Get the list of products from input prediction corpus file and print them line by line to the output"
                            + "file in the argument")
                    .hasArg().longOpt("list-of-products"));
        }
    };

    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(L2PredictionCorpusOperations.class.getCanonicalName(), HELP_MESSAGE, opts,
                    null, true);
            System.exit(1);
        }

        if (cl.hasOption("help")) {
            HELP_FORMATTER.printHelp(L2PredictionCorpusOperations.class.getCanonicalName(), HELP_MESSAGE, opts,
                    null, true);
            System.exit(1);
        }

        if (cl.hasOption(OPTION_WRITE_PRODUCTS_AS_LIST_OF_INCHIS)) {
            L2PredictionCorpus corpus = L2PredictionCorpus.readPredictionsFromJsonFile(
                    new File(cl.getOptionValue(OPTION_WRITE_PRODUCTS_AS_LIST_OF_INCHIS)));
            corpus.writePredictionsAsInchiList(
                    new File(cl.getOptionValue(OPTION_WRITE_PRODUCTS_AS_LIST_OF_INCHIS)));
        }
    }
}