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.biointerpretation.l2expansion; import act.server.MongoDB; import act.shared.Chemical; import chemaxon.struc.Molecule; import com.act.biointerpretation.Utils.ReactionProjector; import com.act.biointerpretation.mechanisminspection.ErosCorpus; import com.act.biointerpretation.sars.SarCorpus; import com.act.jobs.FileChecker; import com.act.jobs.JavaRunnable; 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.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStream; import java.util.ArrayList; import java.util.List; import java.util.Optional; /** * Runs L2 Expansion */ public class L2ExpansionDriver { private static final Logger LOGGER = LogManager.getFormatterLogger(L2ExpansionDriver.class); private static Integer NO_MASS_THRESHOLD = Integer.MAX_VALUE; private static final String OPTION_METABOLITES = "m"; private static final String OPTION_MASS_THRESHOLD = "M"; private static final String OPTION_RO_CORPUS = "c"; private static final String OPTION_RO_IDS = "r"; private static final String OPTION_SAR_CORPUS = "s"; private static final String OPTION_OUTPUT_PATH = "o"; private static final String OPTION_PROGRESS_PATH = "p"; private static final String OPTION_DB = "db"; private static final String OPTION_EXPANSION_TYPE = "t"; private static final String OPTION_ADDITIONAL_CHEMICALS = "p"; private static final String OPTION_HELP = "h"; public static final String HELP_MESSAGE = "This class is used to carry out L2 expansion. It first applies every RO from the input RO list to " + "every metabolite in the input metabolite list. Example input lists can be found on the NAS at " + "MNT_SHARED_DATA/Gil/resources. This creates a list of predicted reactions, which are augmented " + "with chemical ids and names, as well as reaction ids from the database. At the end of the run, " + "the predictions are printed to a json file."; public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() { { add(Option.builder(OPTION_METABOLITES).argName("metabolites path name") .desc("The absolute path to the metabolites file.").hasArg().longOpt("metabolite-file") .required(true)); add(Option.builder(OPTION_MASS_THRESHOLD).argName("mass threshold").desc( "The maximum mass of a substrate, in daltons. Substrates with higher mass will be discarded.") .hasArg().longOpt("mass-threshold").type(Integer.class)); add(Option.builder(OPTION_RO_CORPUS).argName("ro corpus").desc( "The path to the file containing the eros corpus, if not the validation corpus. Ignored if " + "running a SAR expansion.") .hasArg().longOpt("ro-corpus")); add(Option.builder(OPTION_RO_IDS).argName("ro ids path name") .desc("The path to a file containing the RO ids to use. If this option is omitted, " + "all ROs in the corpus are used. Ignored if running a SAR expansion.") .hasArg().longOpt("ro-file")); add(Option.builder(OPTION_SAR_CORPUS).argName("sar corpus").desc( "The path to a file containing the sar corpus to use. Ignored if running an RO-only expansion.") .hasArg().longOpt("sar-corpus")); add(Option.builder(OPTION_RO_IDS).argName("ro ids") .desc("The absolute path to the file containing the RO ids to use. If this option is omitted, " + "all ROs in the corpus are used.") .hasArg().longOpt("ro-ids")); add(Option.builder(OPTION_OUTPUT_PATH).argName("output file path") .desc("The path to the file to which to write the json file of predicted reactions.").hasArg() .longOpt("output-file-path").required(true)); add(Option.builder(OPTION_PROGRESS_PATH).argName("progress file path").desc( "The path to the file to which to write the json file of predicted reactions as each projection runs.") .hasArg().longOpt("progress-file-path")); add(Option.builder(OPTION_DB).argName("db name").desc("The name of the mongo DB to use.").hasArg() .longOpt("db-name")); add(Option.builder(OPTION_EXPANSION_TYPE).argName("type of expansion").desc( "Type can take values: {ONE_SUB, TWO_SUB, SAR}. ONE_SUB and TWO_SUB operate with only ROs, on one " + "and two substrates, respectively, using only ROs. SAR runs an expansion from a SarCorpus, which " + "still applies ROs but additionally constrains the substrates of each RO based on the supplied SARs.") .hasArg().longOpt("expansion-type").required(true)); add(Option.builder(OPTION_ADDITIONAL_CHEMICALS).argName("additional chemicals path name") .desc("The absolute path to the additional chemicals file.").hasArg() .longOpt("additional-chemicals-file")); add(Option.builder(OPTION_HELP).argName("help").desc("Prints this help message.").longOpt("help")); } }; public static final HelpFormatter HELP_FORMATTER = new HelpFormatter(); static { HELP_FORMATTER.setWidth(100); } public static final String LOCAL_HOST = "localhost"; public static final Integer PORT_NUMBER = 27017; public enum ExpansionType { ONE_SUB, TWO_SUB, SAR, } public static void main(String[] args) throws Exception { // Build command line parser. 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(L2ExpansionDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } // Print help. if (cl.hasOption(OPTION_HELP)) { HELP_FORMATTER.printHelp(L2ExpansionDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } // Get output files. String outputPath = cl.getOptionValue(OPTION_OUTPUT_PATH); File outputFile = new File(outputPath); if (outputFile.isDirectory() || outputFile.exists()) { LOGGER.error("Supplied output file is a directory or already exists."); System.exit(1); } outputFile.createNewFile(); File inchiOutputFile = new File(outputPath + ".inchis"); if (inchiOutputFile.isDirectory() || inchiOutputFile.exists()) { LOGGER.error("Supplied inchi output file is a directory or already exists."); System.exit(1); } inchiOutputFile.createNewFile(); Optional<OutputStream> maybeProgressStream = Optional.empty(); if (cl.hasOption(OPTION_PROGRESS_PATH)) { String progressPath = cl.getOptionValue(OPTION_PROGRESS_PATH); File progressFile = new File(progressPath); LOGGER.info("Writing incremental results to file at %s", progressFile.getAbsolutePath()); if (progressFile.isDirectory() || progressFile.exists()) { LOGGER.error("Supplied progress file is a directory or already exists."); System.exit(1); } maybeProgressStream = Optional.of(new FileOutputStream(progressFile)); } // Get metabolite list L2InchiCorpus inchiCorpus = getInchiCorpus(cl, OPTION_METABOLITES); LOGGER.info("%d substrate inchis.", inchiCorpus.getInchiList().size()); Integer maxMass = NO_MASS_THRESHOLD; if (cl.hasOption(OPTION_MASS_THRESHOLD)) { maxMass = Integer.parseInt(cl.getOptionValue(OPTION_MASS_THRESHOLD)); LOGGER.info("Filtering out substrates with mass more than %d daltons.", maxMass); } inchiCorpus.filterByMass(maxMass); LOGGER.info("%d substrate inchis that are importable as molecules.", inchiCorpus.getInchiList().size()); PredictionGenerator generator = new AllPredictionsGenerator(new ReactionProjector()); L2Expander expander = buildExpander(cl, inchiCorpus, generator); L2PredictionCorpus predictionCorpus = expander.getPredictions(maybeProgressStream); LOGGER.info("Done with L2 expansion. Produced %d predictions.", predictionCorpus.getCorpus().size()); LOGGER.info("Writing corpus to file."); predictionCorpus.writePredictionsToJsonFile(outputFile); L2InchiCorpus productInchis = new L2InchiCorpus(predictionCorpus.getUniqueProductInchis()); productInchis.writeToFile(inchiOutputFile); LOGGER.info("L2ExpansionDriver complete!"); } private static L2Expander buildExpander(CommandLine cl, L2InchiCorpus inchiCorpus, PredictionGenerator generator) throws IOException { ExpansionType expansionType = ExpansionType.valueOf(cl.getOptionValue(OPTION_EXPANSION_TYPE)); switch (expansionType) { case ONE_SUB: LOGGER.info("Running one substrate expansion"); return new SingleSubstrateRoExpander(getRoCorpus(cl), inchiCorpus.getMolecules(), generator); case TWO_SUB: LOGGER.info("Running two substrate expansion."); LOGGER.warn("This functionality is still experimental as it is not currently tested."); if (!cl.hasOption(OPTION_ADDITIONAL_CHEMICALS)) { LOGGER.error("Must supply additional chemicals file for two substrate expansion."); System.exit(1); } MongoDB mongoDB = new MongoDB(LOCAL_HOST, PORT_NUMBER, cl.getOptionValue(OPTION_DB)); // Start mongo instance. L2InchiCorpus chemicalInchis = getInchiCorpus(cl, OPTION_ADDITIONAL_CHEMICALS); List<Chemical> chemicalsOfInterest = L2ExpansionDriver .convertListOfInchisToMolecules(chemicalInchis.getInchiList(), mongoDB); List<Chemical> metaboliteChemicals = L2ExpansionDriver .convertListOfInchisToMolecules(inchiCorpus.getInchiList(), mongoDB); return new TwoSubstrateRoExpander(chemicalsOfInterest, metaboliteChemicals, getRoCorpus(cl), generator); case SAR: LOGGER.info("Running sar-based expansion."); File sarCorpusFile = new File(cl.getOptionValue(OPTION_SAR_CORPUS)); if (!sarCorpusFile.exists() || sarCorpusFile.isDirectory()) { LOGGER.error("Sar corpus is not a valid file."); System.exit(1); } SarCorpus sarCorpus = SarCorpus.readCorpusFromJsonFile(sarCorpusFile); return new SingleSubstrateSarExpander(sarCorpus, inchiCorpus.getMolecules(), generator); default: throw new IllegalArgumentException("Invalid expansion type."); } } private static ErosCorpus getRoCorpus(CommandLine cl) throws IOException { ErosCorpus eroCorpus = new ErosCorpus(); if (cl.hasOption(OPTION_RO_CORPUS)) { File roCorpusFile = new File(cl.getOptionValue(OPTION_RO_CORPUS)); if (!roCorpusFile.exists()) { LOGGER.error("Ro corpus file does not exist."); System.exit(1); } FileInputStream roInputStream = new FileInputStream(roCorpusFile); eroCorpus.loadCorpus(roInputStream); } else { eroCorpus.loadValidationCorpus(); } if (cl.hasOption(OPTION_RO_IDS)) { LOGGER.info("Filtering corpus by RO list from rosFile."); File roIdsFile = new File(cl.getOptionValue(OPTION_RO_IDS)); if (!roIdsFile.exists()) { LOGGER.error("Ro ids file does not exist."); System.exit(1); } eroCorpus.filterCorpusByIdFile(roIdsFile); } else { LOGGER.info("Leaving all ROs in corpus."); } return eroCorpus; } /** * Gets a list of inchis for a command line option that points to a file with one inchi per line. * * @param cl Command line parser. * @param optionForFileName Option for a file with one inchi per line. Either the metabolite list or addition * chemical list. * @return The list of inchis contained in the file. * @throws IOException */ private static L2InchiCorpus getInchiCorpus(CommandLine cl, String optionForFileName) throws IOException { File inchisFile = new File(cl.getOptionValue(optionForFileName)); LOGGER.info("Getting inchi list from %s", inchisFile); L2InchiCorpus inchiCorpus = new L2InchiCorpus(); inchiCorpus.loadCorpus(inchisFile); return inchiCorpus; } /** * This function constructs a mapping between inchi and its chemical representation. * * @param inchis A list of inchis * @param mongoDB The db from which to get the chemical entry * @return A map of inchi to chemical */ private static List<Chemical> convertListOfInchisToMolecules(List<String> inchis, MongoDB mongoDB) { List<Chemical> result = new ArrayList<>(); for (String inchi : inchis) { result.add(mongoDB.getChemicalFromInChI(inchi)); } return result; } /** * Wraps L2 expansion so that it can be used in a workflow. The inputs are a list of RO IDs to expand on, * a file containing the substrates to apply the ROs to, and a file to which to write the output prediction corpus. * * @param roIds * @param substrateListFile * @param outputFile * @return */ public static JavaRunnable getRunnableOneSubstrateRoExpander(List<Integer> roIds, File substrateListFile, File outputFile) { return new JavaRunnable() { @Override public void run() throws IOException { // Verify files FileChecker.verifyInputFile(substrateListFile); FileChecker.verifyAndCreateOutputFile(outputFile); // Handle input ros ErosCorpus roCorpus = new ErosCorpus(); roCorpus.loadValidationCorpus(); roCorpus.filterCorpusById(roIds); // Handle input substrates L2InchiCorpus inchis = new L2InchiCorpus(); inchis.loadCorpus(substrateListFile); List<Molecule> moleculeList = inchis.getMolecules(); // Build expander PredictionGenerator generator = new AllPredictionsGenerator(new ReactionProjector()); L2Expander expander = new SingleSubstrateRoExpander(roCorpus, moleculeList, generator); // Run expander L2PredictionCorpus predictions = expander.getPredictions(); // Write output predictions.writePredictionsToJsonFile(outputFile); } @Override public String toString() { return "oneSubstrateRoExpander:" + roIds.toString(); } }; } }