com.act.utils.parser.UniprotInterpreter.java Source code

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Here is the source code for com.act.utils.parser.UniprotInterpreter.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.utils.parser;

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 org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava.nbio.core.sequence.loader.UniprotProxySequenceReader;
import org.biojava.nbio.core.util.XMLHelper;
import org.w3c.dom.Document;
import org.xml.sax.SAXException;

import javax.xml.parsers.ParserConfigurationException;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

public class UniprotInterpreter {

    private static final Logger LOGGER = LogManager.getFormatterLogger(GenbankInterpreter.class);
    private static final String OPTION_UNIPROT_PATH = "p";

    public static final String HELP_MESSAGE = StringUtils.join(new String[] {
            "This class parses Uniprot Protein sequence files. It can be used on the command line with ",
            "a file path as a parameter." }, "");

    public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {
        {
            add(Option.builder(OPTION_UNIPROT_PATH).argName("uniprot file")
                    .desc("uniprot protein sequence file containing sequence and annotations").hasArg()
                    .longOpt("uniprot").required());
            add(Option.builder("h").argName("help").desc("Example of usage: -p filepath.xml").longOpt("help"));
        }
    };

    public static final HelpFormatter HELP_FORMATTER = new HelpFormatter();

    static {
        HELP_FORMATTER.setWidth(100);
    }

    private File xmlFile;
    private Document xmlDocument;
    private ProteinSequence seq;

    public void init() throws IOException, SAXException, ParserConfigurationException, CompoundNotFoundException {
        BufferedReader br = new BufferedReader(new FileReader(xmlFile));
        String line;
        StringBuilder sb = new StringBuilder();

        while ((line = br.readLine()) != null) {
            sb.append(line.trim());
        }

        xmlDocument = XMLHelper.inputStreamToDocument(new ByteArrayInputStream(sb.toString().getBytes()));

        AminoAcidCompoundSet aminoAcidCompoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();

        UniprotProxySequenceReader uniprotProxySequenceReader = new UniprotProxySequenceReader(xmlDocument,
                aminoAcidCompoundSet);

        seq = new ProteinSequence(uniprotProxySequenceReader);
    }

    private void checkInit() {
        if (xmlDocument == null || seq == null) {
            String msg = "Class hasn't been appropriately initialized, no Document and/or ProteinSequence object";
            LOGGER.error(msg);
            throw new RuntimeException(msg);
        }
    }

    public UniprotInterpreter(File uniprotFile) {
        xmlFile = uniprotFile;
    }

    public Document getXmlDocument() {
        checkInit();
        return this.xmlDocument;
    }

    public String getSequence() {
        checkInit();
        return seq.getSequenceAsString();
    }

    public static void main(String[] args)
            throws ParserConfigurationException, IOException, SAXException, CompoundNotFoundException {
        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(UniprotInterpreter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
            System.exit(1);
        }

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

        File uniprotFile = new File(cl.getOptionValue(OPTION_UNIPROT_PATH));

        if (!uniprotFile.exists()) {
            String msg = "Uniprot file path is null";
            LOGGER.error(msg);
            throw new RuntimeException(msg);
        } else {
            UniprotInterpreter reader = new UniprotInterpreter(uniprotFile);
            reader.init();
        }
    }

}