Java tutorial
/************************************************************************* * * * 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); } } }