/*************************************************************************
* *
* 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.cofactorremoval;
import act.server.NoSQLAPI;
import act.shared.Reaction;
import com.act.biointerpretation.desalting.ReactionDesalter;
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.commons.lang3.tuple.Pair;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.util.ArrayList;
import java.util.List;
public class ReactionCofactorRemover {
private static final Logger LOGGER = LogManager.getFormatterLogger(ReactionCofactorRemover.class);
public static final String OPTION_READ_DB = "d";
public static final String OPTION_RXN_ID = "r";
public static final String HELP_MESSAGE = StringUtils.join(new String[]{
"This class removes cofactors from a single reaction and prints the results to stdout. ",
"To remove cofactors from an entire installer DB, use BiointerpretationDriver."
}, "");
public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() {{
add(Option.builder(OPTION_READ_DB)
.argName("read db name")
.desc("The name of the read DB to use")
.hasArg().required()
.longOpt("db")
);
add(Option.builder(OPTION_RXN_ID)
.argName("id")
.desc("The id of the reaction from which to remove cofactors")
.hasArg().required()
.longOpt("id")
);
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 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;
}
NoSQLAPI api = new NoSQLAPI(cl.getOptionValue(OPTION_READ_DB), cl.getOptionValue(OPTION_READ_DB));
CofactorRemover cofactorRemover = new CofactorRemover(api);
cofactorRemover.init();
Pair<Reaction, Reaction> results = cofactorRemover.removeCofactorsFromOneReaction(
Long.parseLong(cl.getOptionValue(OPTION_RXN_ID)));
System.out.format("Reaction before processing:\n");
printReport(results.getLeft());
System.out.println();
System.out.format("Reaction after processing:\n");
printReport(results.getRight());
System.out.println();
}
private static void printReport(Reaction rxn) {
System.out.format("Reaction before processing:\n");
System.out.format(" Substrates: %s\n", StringUtils.join(rxn.getSubstrates(), ", "));
System.out.format(" Products: %s\n", StringUtils.join(rxn.getProducts(), ", "));
System.out.format(" Sub. cofactors: %s\n", StringUtils.join(rxn.getSubstrateCofactors(), ", "));
System.out.format(" Prod. cofactors: %s\n", StringUtils.join(rxn.getProductCofactors(), ", "));
System.out.format(" Coenzymes: %s\n", StringUtils.join(rxn.getCoenzymes(), ", "));
}
}