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.sars; import act.server.MongoDB; import act.shared.Seq; 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.util.ArrayList; import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; /** * A sequence grouper that iterates over the seq DB and groups only seq entries that have exactly same sequence. */ public class SeqDBReactionGrouper { private static final Logger LOGGER = LogManager.getFormatterLogger(SeqDBReactionGrouper.class); private static final String OPTION_DB = "db"; private static final String OPTION_OUTPUT_PATH = "o"; private static final String OPTION_LIMIT = "l"; private static final String OPTION_HELP = "h"; public static final String HELP_MESSAGE = "This class is used to generate reaction groups by scanning the seq DB for sequences that point to multiple " + "reactions. Options are supplied to indicate how far into the DB to scan, which DB to use, and where to " + "write the output."; public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() { { add(Option.builder(OPTION_DB).argName("db name").desc("The name of the mongo DB to use.").hasArg() .longOpt("db-name").required(true)); add(Option.builder(OPTION_OUTPUT_PATH).argName("output file path").desc( "The absolute path to the file to which to write the json file of the reaction group corpus.") .hasArg().longOpt("output-file-path").required(true)); add(Option.builder(OPTION_LIMIT).argName("seq limit").desc( "The maximum number of seq entries to process. This is useful because running on the entire DB can " + "require a lot of time and memory.") .hasArg().longOpt("seq-limit").type(Integer.class)); 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); } private static final String LOCAL_HOST = "localhost"; private static final Integer MONGO_PORT = 27017; private static final Integer DEFAULT_LIMIT_INFINITY = Integer.MAX_VALUE; 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(SeqDBReactionGrouper.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } // Print help. if (cl.hasOption(OPTION_HELP)) { HELP_FORMATTER.printHelp(SeqDBReactionGrouper.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } // Handle arguments String mongoDBName = cl.getOptionValue(OPTION_DB); MongoDB mongoDB = new MongoDB(LOCAL_HOST, MONGO_PORT, mongoDBName); File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_PATH)); if (outputFile.isDirectory() || outputFile.exists()) { LOGGER.error("Supplied output file is a directory or already exists."); System.exit(1); } outputFile.createNewFile(); Integer limit = DEFAULT_LIMIT_INFINITY; if (cl.hasOption(OPTION_LIMIT)) { limit = Integer.parseInt(cl.getOptionValue(OPTION_LIMIT)); } LOGGER.info("Only processing first %d entries in Seq DB.", limit); SeqDBReactionGrouper enzymeGrouper = new SeqDBReactionGrouper(mongoDB.getSeqIterator(), mongoDBName, limit); LOGGER.info("Scanning seq db for reactions with same seq."); ReactionGroupCorpus groupCorpus = enzymeGrouper.getReactionGroupCorpus(); LOGGER.info("Writing output to file."); groupCorpus.printToJsonFile(outputFile); LOGGER.info("Complete!"); } final Integer limit; final String dbName; final Iterator<Seq> seqIterator; /** * Builds a SeqDBReactionGrouper for the given Seq entries. * * @param seqIterator The Seq entries to group. * @param limit The maximum number of entries to process. This can be used to limit memory and time. */ public SeqDBReactionGrouper(Iterator<Seq> seqIterator, String dbName, Integer limit) { this.seqIterator = seqIterator; this.dbName = dbName; this.limit = limit; } /** * Builds a SeqDBReactionGrouper for the given Seq entries. * * @param seqIterator The Seq entries to group. */ public SeqDBReactionGrouper(Iterator<Seq> seqIterator, String dbName) { this(seqIterator, dbName, DEFAULT_LIMIT_INFINITY); } /** * Returns the collection of SeqGroups produced by running this grouper on the Seq entries from the DB. * TODO: Implement this in a way that doesn't store the whole map in memory at the same time. * * @return The collection of produced SeqGroups. */ public ReactionGroupCorpus getReactionGroupCorpus() { Map<String, ReactionGroup> sequenceToReactionGroupMap = getSequenceToReactionGroupMap(seqIterator); LOGGER.info("Done getting seq group map, found %d distinct SeqGroups.", sequenceToReactionGroupMap.size()); return new ReactionGroupCorpus(sequenceToReactionGroupMap.values()); } /** * Iterates over seq entries and builds a map from unique sequences to ReactionGroup objects that list their * corresponding Seq entry ids and Reaction ids. * * @param seqIterator * @return */ private Map<String, ReactionGroup> getSequenceToReactionGroupMap(Iterator<Seq> seqIterator) { Map<String, ReactionGroup> sequenceToReactionGroupMap = new HashMap<>(); Integer counter = 0; while (seqIterator.hasNext()) { if (counter >= limit) { break; } if (counter % 1000 == 0) { LOGGER.info("Processed %d seq entries so far", counter); } Seq seq = seqIterator.next(); String sequence = seq.getSequence(); ReactionGroup group = sequenceToReactionGroupMap.get(sequence); if (group == null) { group = new ReactionGroup("SEQ_ID_" + Integer.toString(seq.getUUID()), dbName); sequenceToReactionGroupMap.put(sequence, group); } for (Long reactionId : seq.getReactionsCatalyzed()) { group.addReactionId(reactionId); } counter++; } return sequenceToReactionGroupMap; } }