com.act.lcms.v2.TraceIndexAnalyzer.java Source code

Java tutorial

Introduction

Here is the source code for com.act.lcms.v2.TraceIndexAnalyzer.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.lcms.v2;

import com.act.lcms.XZ;
import com.act.lcms.db.analysis.WaveformAnalysis;
import com.act.lcms.db.model.MS1ScanForWellAndMassCharge;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.databind.ObjectMapper;
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 org.rocksdb.RocksDBException;

import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

public class TraceIndexAnalyzer {
    private static final Logger LOGGER = LogManager.getFormatterLogger(TraceIndexAnalyzer.class);
    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();

    private static final String OPTION_INDEX_PATH = "x";
    private static final String OPTION_OUTPUT_PATH = "o";

    public static final String HELP_MESSAGE = StringUtils.join(new String[] {
            "This class consumes windowed traces from an LCMS scan files, searching each window for peaks and writing the ",
            "results of its analysis in a large JSON document." }, "");

    public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {
        {
            add(Option.builder(OPTION_INDEX_PATH).argName("index path")
                    .desc("A path to the directory where the on-disk index is stored; must already exist").hasArg()
                    .required().longOpt("index"));
            add(Option.builder(OPTION_OUTPUT_PATH).argName("outputpath")
                    .desc("A path where the SNR/time/intensity results per window should be written as JSON")
                    .hasArg().required().longOpt("output"));
            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 class AnalysisResult {
        @JsonProperty("mz")
        private Double mz;

        @JsonProperty("peak_intensity")
        private Double peakIntensity;

        @JsonProperty("peak_time")
        private Double peakTime;

        protected AnalysisResult() {
        }

        public AnalysisResult(Double mz, Double peakIntensity, Double peakTime) {
            this.mz = mz;
            this.peakIntensity = peakIntensity;
            this.peakTime = peakTime;
        }

        public Double getMz() {
            return mz;
        }

        protected void setMz(Double mz) {
            this.mz = mz;
        }

        public Double getPeakIntensity() {
            return peakIntensity;
        }

        protected void setPeakIntensity(Double peakIntensity) {
            this.peakIntensity = peakIntensity;
        }

        public Double getPeakTime() {
            return peakTime;
        }

        protected void setPeakTime(Double peakTime) {
            this.peakTime = peakTime;
        }
    }

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

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

        File rocksDBFile = new File(cl.getOptionValue(OPTION_INDEX_PATH));
        if (!rocksDBFile.exists()) {
            System.err.format("Index file at %s does not exist, nothing to analyze", rocksDBFile.getAbsolutePath());
            HELP_FORMATTER.printHelp(TraceIndexExtractor.class.getCanonicalName(), HELP_MESSAGE, opts, null, true);
            System.exit(1);
        }

        LOGGER.info("Starting analysis");

        TraceIndexAnalyzer analyzer = new TraceIndexAnalyzer();
        analyzer.runExtraction(rocksDBFile, new File(cl.getOptionValue(OPTION_OUTPUT_PATH)));

        LOGGER.info("Done");
    }

    private void runExtraction(File rocksDBFile, File outputFile) throws RocksDBException, IOException {
        List<AnalysisResult> results = new ArrayList<>();

        // Extract each target's trace, computing and saving stats as we go.  This should fit in memory no problem.
        Iterator<Pair<Double, List<XZ>>> traceIterator = new TraceIndexExtractor()
                .getIteratorOverTraces(rocksDBFile);
        while (traceIterator.hasNext()) {
            Pair<Double, List<XZ>> targetAndTrace = traceIterator.next();

            String label = String.format("%.6f", targetAndTrace.getLeft());

            // Note: here we cheat by knowing how the MS1 class is going to use this incredibly complex container.
            MS1ScanForWellAndMassCharge scanForWell = new MS1ScanForWellAndMassCharge();
            scanForWell.setMetlinIons(Collections.singletonList(label));
            scanForWell.getIonsToSpectra().put(label, targetAndTrace.getRight());

            Pair<List<XZ>, Map<Double, Double>> timeWindowsAndMaxes = WaveformAnalysis
                    .compressIntensityAndTimeGraphsAndFindMaxIntensityInEveryTimeWindow(targetAndTrace.getRight(),
                            WaveformAnalysis.COMPRESSION_CONSTANT);
            List<XZ> calledPeaks = WaveformAnalysis.detectPeaksInIntensityTimeWaveform(
                    timeWindowsAndMaxes.getLeft(), WaveformAnalysis.PEAK_DETECTION_THRESHOLD); // Same as waveform analysis.

            for (XZ calledPeak : calledPeaks) {
                AnalysisResult result = new AnalysisResult(targetAndTrace.getLeft(),
                        timeWindowsAndMaxes.getRight().get(calledPeak.getTime()), calledPeak.getTime());

                results.add(result);
            }
        }

        LOGGER.info("Writing window stats to JSON file");
        try (FileOutputStream fos = new FileOutputStream(outputFile)) {
            OBJECT_MAPPER.writerWithDefaultPrettyPrinter().writeValue(fos, results);
        }
    }
}