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.desalting; import chemaxon.license.LicenseProcessingException; import chemaxon.reaction.ReactionException; import com.act.biointerpretation.Utils.ReactionProjector; import com.act.lcms.db.io.LoadPlateCompositionIntoDB; 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 java.io.BufferedReader; import java.io.BufferedWriter; import java.io.File; import java.io.FileReader; import java.io.FileWriter; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.List; import java.util.Map; public class ChemicalDesalter { private static final Logger LOGGER = LogManager.getFormatterLogger(ChemicalDesalter.class); public static final String OPTION_OUTPUT_PREFIX = "o"; public static final String OPTION_INCHI_INPUT_LIST = "i"; public static final String HELP_MESSAGE = StringUtils.join(new String[] { "This class desalts a list of InChIs and outputs the results to a file. To desalt an entire installer DB, ", "use BiointerpretationDriver." }, ""); public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() { { add(Option.builder(OPTION_OUTPUT_PREFIX).argName("output prefix") .desc("A prefix for the output data/pdf files").hasArg().required().longOpt("output-prefix")); add(Option.builder(OPTION_INCHI_INPUT_LIST).argName("inchi list file") .desc("A file containing a list of InChIs to desalt").hasArg().required() .longOpt("input-inchis")); 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); } private Desalter desalter = new Desalter(new ReactionProjector()); 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(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(ReactionDesalter.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } ChemicalDesalter runner = new ChemicalDesalter(); String outAnalysis = cl.getOptionValue(OPTION_OUTPUT_PREFIX); if (cl.hasOption(OPTION_INCHI_INPUT_LIST)) { File inputFile = new File(cl.getOptionValue(OPTION_INCHI_INPUT_LIST)); if (!inputFile.exists()) { System.err.format("Cannot find input file at %s\n", inputFile.getAbsolutePath()); HELP_FORMATTER.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } runner.exampleChemicalsList(outAnalysis, inputFile); } } public ChemicalDesalter() { } public void exampleChemicalsList(String outputPrefix, File inputFile) throws IOException, LicenseProcessingException, ReactionException { desalter.initReactors(); List<String> inchis = new ArrayList<>(); try (BufferedReader reader = new BufferedReader(new FileReader(inputFile))) { String line; // Slurp in the list of InChIs from the input file. while ((line = reader.readLine()) != null) { inchis.add(line.trim()); } } generateAnalysisOfDesaltingSaltyChemicals(inchis, outputPrefix); } /** * This function bins each reaction into modified, unchanged, errors and complex files based on * processing them through the desalter module. * * @param salties A list of reactions * @param outputPrefix The output prefix for the generated files */ private void generateAnalysisOfDesaltingSaltyChemicals(List<String> salties, String outputPrefix) { try (BufferedWriter substrateModifiedFileWriter = new BufferedWriter( new FileWriter(new File(outputPrefix + "_modified.txt"))); BufferedWriter substrateUnchangedFileWriter = new BufferedWriter( new FileWriter(new File(outputPrefix + "_unchanged.txt"))); BufferedWriter substrateErrorsFileWriter = new BufferedWriter( new FileWriter(new File(outputPrefix + "_errors.txt"))); BufferedWriter substrateComplexFileWriter = new BufferedWriter( new FileWriter(new File(outputPrefix + "_complex.txt")))) { for (int i = 0; i < salties.size(); i++) { String salty = salties.get(i); String saltySmile = null; try { saltySmile = desalter.InchiToSmiles(salty); } catch (Exception err) { LOGGER.error( String.format("Exception caught while desalting inchi: %s with error message: %s\n", salty, err.getMessage())); substrateErrorsFileWriter.write("InchiToSmiles1\t" + salty); substrateErrorsFileWriter.newLine(); continue; } Map<String, Integer> results = null; try { results = desalter.desaltInchi(salty); } catch (Exception err) { LOGGER.error( String.format("Exception caught while desalting inchi: %s with error message: %s\n", salty, err.getMessage())); substrateErrorsFileWriter.append("cleaned\t" + salty); substrateErrorsFileWriter.newLine(); continue; } //Not sure results can be size zero or null, but check anyway if (results == null) { LOGGER.error(String.format("Clean results are null for chemical: %s\n", salty)); substrateErrorsFileWriter.append("clean results are null:\t" + salty); substrateErrorsFileWriter.newLine(); continue; } if (results.isEmpty()) { LOGGER.error(String.format("Clean results are empty for chemical: %s\n", salty)); substrateErrorsFileWriter.append("clean results are empty:\t" + salty); substrateErrorsFileWriter.newLine(); continue; } //If cleaning resulted in a single organic product if (results.size() == 1) { String cleaned = results.keySet().iterator().next(); String cleanSmile = null; try { cleanSmile = desalter.InchiToSmiles(cleaned); } catch (Exception err) { LOGGER.error( String.format("Exception caught while desalting inchi: %s with error message: %s\n", cleaned, err.getMessage())); substrateErrorsFileWriter.append("InchiToSmiles2\t" + salty); substrateErrorsFileWriter.newLine(); } if (!salty.equals(cleaned)) { String[] stringElements = { salty, cleaned, saltySmile, cleanSmile }; substrateModifiedFileWriter.append(StringUtils.join(Arrays.asList(stringElements), "\t")); substrateModifiedFileWriter.newLine(); } else { String[] stringElements = { salty, saltySmile }; substrateUnchangedFileWriter.append(StringUtils.join(Arrays.asList(stringElements), "\t")); substrateUnchangedFileWriter.newLine(); } } else { //Otherwise there were multiple organic products substrateComplexFileWriter.append(">>\t" + salty + "\t" + saltySmile); substrateComplexFileWriter.newLine(); for (String inchi : results.keySet()) { substrateComplexFileWriter.append("\t" + inchi + "\t" + desalter.InchiToSmiles(inchi)); substrateComplexFileWriter.newLine(); } } } } catch (IOException exception) { LOGGER.error(String.format("IOException: %s", exception.getMessage())); } } }