Example usage for java.io FileWriter FileWriter

List of usage examples for java.io FileWriter FileWriter

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Introduction

In this page you can find the example usage for java.io FileWriter FileWriter.

Prototype

public FileWriter(FileDescriptor fd)

Source Link

Document

Constructs a FileWriter given a file descriptor, using the platform's java.nio.charset.Charset#defaultCharset() default charset .

Usage

From source file:eqtlmappingpipeline.util.ModuleEqtlGeuvadisReplication.java

/**
 * @param args the command line arguments
 *///from  www . j a va 2  s. c  om
public static void main(String[] args) throws IOException, LdCalculatorException {

    System.out.println(HEADER);
    System.out.println();
    System.out.flush(); //flush to make sure header is before errors
    try {
        Thread.sleep(25); //Allows flush to complete
    } catch (InterruptedException ex) {
    }

    CommandLineParser parser = new PosixParser();
    final CommandLine commandLine;
    try {
        commandLine = parser.parse(OPTIONS, args, true);
    } catch (ParseException ex) {
        System.err.println("Invalid command line arguments: " + ex.getMessage());
        System.err.println();
        new HelpFormatter().printHelp(" ", OPTIONS);
        System.exit(1);
        return;
    }

    final String[] genotypesBasePaths = commandLine.getOptionValues("g");
    final RandomAccessGenotypeDataReaderFormats genotypeDataType;
    final String replicationQtlFilePath = commandLine.getOptionValue("e");
    final String interactionQtlFilePath = commandLine.getOptionValue("i");
    final String outputFilePath = commandLine.getOptionValue("o");
    final double ldCutoff = Double.parseDouble(commandLine.getOptionValue("ld"));
    final int window = Integer.parseInt(commandLine.getOptionValue("w"));

    System.out.println("Genotype: " + Arrays.toString(genotypesBasePaths));
    System.out.println("Interaction file: " + interactionQtlFilePath);
    System.out.println("Replication file: " + replicationQtlFilePath);
    System.out.println("Output: " + outputFilePath);
    System.out.println("LD: " + ldCutoff);
    System.out.println("Window: " + window);

    try {
        if (commandLine.hasOption("G")) {
            genotypeDataType = RandomAccessGenotypeDataReaderFormats
                    .valueOf(commandLine.getOptionValue("G").toUpperCase());
        } else {
            if (genotypesBasePaths[0].endsWith(".vcf")) {
                System.err.println(
                        "Only vcf.gz is supported. Please see manual on how to do create a vcf.gz file.");
                System.exit(1);
                return;
            }
            try {
                genotypeDataType = RandomAccessGenotypeDataReaderFormats
                        .matchFormatToPath(genotypesBasePaths[0]);
            } catch (GenotypeDataException e) {
                System.err
                        .println("Unable to determine input 1 type based on specified path. Please specify -G");
                System.exit(1);
                return;
            }
        }
    } catch (IllegalArgumentException e) {
        System.err.println("Error parsing --genotypesFormat \"" + commandLine.getOptionValue("G")
                + "\" is not a valid input data format");
        System.exit(1);
        return;
    }

    final RandomAccessGenotypeData genotypeData;

    try {
        genotypeData = genotypeDataType.createFilteredGenotypeData(genotypesBasePaths, 100, null, null, null,
                0.8);
    } catch (TabixFileNotFoundException e) {
        LOGGER.fatal("Tabix file not found for input data at: " + e.getPath() + "\n"
                + "Please see README on how to create a tabix file");
        System.exit(1);
        return;
    } catch (IOException e) {
        LOGGER.fatal("Error reading input data: " + e.getMessage(), e);
        System.exit(1);
        return;
    } catch (IncompatibleMultiPartGenotypeDataException e) {
        LOGGER.fatal("Error combining the impute genotype data files: " + e.getMessage(), e);
        System.exit(1);
        return;
    } catch (GenotypeDataException e) {
        LOGGER.fatal("Error reading input data: " + e.getMessage(), e);
        System.exit(1);
        return;
    }

    ChrPosTreeMap<ArrayList<EQTL>> replicationQtls = new QTLTextFile(replicationQtlFilePath, false)
            .readQtlsAsTreeMap();

    int interactionSnpNotInGenotypeData = 0;
    int noReplicationQtlsInWindow = 0;
    int noReplicationQtlsInLd = 0;
    int multipleReplicationQtlsInLd = 0;
    int replicationTopSnpNotInGenotypeData = 0;

    final CSVWriter outputWriter = new CSVWriter(new FileWriter(new File(outputFilePath)), '\t', '\0');
    final String[] outputLine = new String[14];
    int c = 0;
    outputLine[c++] = "Chr";
    outputLine[c++] = "Pos";
    outputLine[c++] = "SNP";
    outputLine[c++] = "Gene";
    outputLine[c++] = "Module";
    outputLine[c++] = "DiscoveryZ";
    outputLine[c++] = "ReplicationZ";
    outputLine[c++] = "DiscoveryZCorrected";
    outputLine[c++] = "ReplicationZCorrected";
    outputLine[c++] = "DiscoveryAlleleAssessed";
    outputLine[c++] = "ReplicationAlleleAssessed";
    outputLine[c++] = "bestLd";
    outputLine[c++] = "bestLd_dist";
    outputLine[c++] = "nextLd";
    outputWriter.writeNext(outputLine);

    HashSet<String> notFound = new HashSet<>();

    CSVReader interactionQtlReader = new CSVReader(new FileReader(interactionQtlFilePath), '\t');
    interactionQtlReader.readNext();//skip header
    String[] interactionQtlLine;
    while ((interactionQtlLine = interactionQtlReader.readNext()) != null) {

        String snp = interactionQtlLine[1];
        String chr = interactionQtlLine[2];
        int pos = Integer.parseInt(interactionQtlLine[3]);
        String gene = interactionQtlLine[4];
        String alleleAssessed = interactionQtlLine[9];
        String module = interactionQtlLine[12];
        double discoveryZ = Double.parseDouble(interactionQtlLine[10]);

        GeneticVariant interactionQtlVariant = genotypeData.getSnpVariantByPos(chr, pos);

        if (interactionQtlVariant == null) {
            System.err.println("Interaction QTL SNP not found in genotype data: " + chr + ":" + pos);
            ++interactionSnpNotInGenotypeData;
            continue;
        }

        EQTL bestMatch = null;
        double bestMatchR2 = Double.NaN;
        Ld bestMatchLd = null;
        double nextBestR2 = Double.NaN;

        ArrayList<EQTL> sameSnpQtls = replicationQtls.get(chr, pos);

        if (sameSnpQtls != null) {
            for (EQTL sameSnpQtl : sameSnpQtls) {
                if (sameSnpQtl.getProbe().equals(gene)) {
                    bestMatch = sameSnpQtl;
                    bestMatchR2 = 1;
                }
            }
        }

        NavigableMap<Integer, ArrayList<EQTL>> potentionalReplicationQtls = replicationQtls.getChrRange(chr,
                pos - window, true, pos + window, true);

        for (ArrayList<EQTL> potentialReplicationQtls : potentionalReplicationQtls.values()) {

            for (EQTL potentialReplicationQtl : potentialReplicationQtls) {

                if (!potentialReplicationQtl.getProbe().equals(gene)) {
                    continue;
                }

                GeneticVariant potentialReplicationQtlVariant = genotypeData.getSnpVariantByPos(
                        potentialReplicationQtl.getRsChr().toString(), potentialReplicationQtl.getRsChrPos());

                if (potentialReplicationQtlVariant == null) {
                    notFound.add(potentialReplicationQtl.getRsChr().toString() + ":"
                            + potentialReplicationQtl.getRsChrPos());
                    ++replicationTopSnpNotInGenotypeData;
                    continue;
                }

                Ld ld = interactionQtlVariant.calculateLd(potentialReplicationQtlVariant);
                double r2 = ld.getR2();

                if (r2 > 1) {
                    r2 = 1;
                }

                if (bestMatch == null) {
                    bestMatch = potentialReplicationQtl;
                    bestMatchR2 = r2;
                    bestMatchLd = ld;
                } else if (r2 > bestMatchR2) {
                    bestMatch = potentialReplicationQtl;
                    nextBestR2 = bestMatchR2;
                    bestMatchR2 = r2;
                    bestMatchLd = ld;
                }

            }
        }

        double replicationZ = Double.NaN;
        double replicationZCorrected = Double.NaN;
        double discoveryZCorrected = Double.NaN;

        String replicationAlleleAssessed = null;

        if (bestMatch != null) {
            replicationZ = bestMatch.getZscore();
            replicationAlleleAssessed = bestMatch.getAlleleAssessed();

            if (pos != bestMatch.getRsChrPos()) {

                String commonHap = null;
                double commonHapFreq = -1;
                for (Map.Entry<String, Double> hapFreq : bestMatchLd.getHaplotypesFreq().entrySet()) {

                    double f = hapFreq.getValue();

                    if (f > commonHapFreq) {
                        commonHapFreq = f;
                        commonHap = hapFreq.getKey();
                    }

                }

                String[] commonHapAlleles = StringUtils.split(commonHap, '/');

                discoveryZCorrected = commonHapAlleles[0].equals(alleleAssessed) ? discoveryZ : discoveryZ * -1;
                replicationZCorrected = commonHapAlleles[1].equals(replicationAlleleAssessed) ? replicationZ
                        : replicationZ * -1;

            } else {

                discoveryZCorrected = discoveryZ;
                replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) ? replicationZ
                        : replicationZ * -1;

            }

        }

        c = 0;
        outputLine[c++] = chr;
        outputLine[c++] = String.valueOf(pos);
        outputLine[c++] = snp;
        outputLine[c++] = gene;
        outputLine[c++] = module;
        outputLine[c++] = String.valueOf(discoveryZ);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZ);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(discoveryZCorrected);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(replicationZCorrected);
        outputLine[c++] = alleleAssessed;
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.getAlleleAssessed());
        outputLine[c++] = String.valueOf(bestMatchR2);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getRsChrPos()));
        outputLine[c++] = String.valueOf(nextBestR2);
        outputWriter.writeNext(outputLine);

    }

    outputWriter.close();

    for (String e : notFound) {
        System.err.println("Not found: " + e);
    }

    System.out.println("interactionSnpNotInGenotypeData: " + interactionSnpNotInGenotypeData);
    System.out.println("noReplicationQtlsInWindow: " + noReplicationQtlsInWindow);
    System.out.println("noReplicationQtlsInLd: " + noReplicationQtlsInLd);
    System.out.println("multipleReplicationQtlsInLd: " + multipleReplicationQtlsInLd);
    System.out.println("replicationTopSnpNotInGenotypeData: " + replicationTopSnpNotInGenotypeData);

}

From source file:POP3Mail.java

public static void main(String[] args) {
    try {//www  .j  a v a  2s. com
        LogManager.getLogManager().readConfiguration(new FileInputStream("logging.properties"));
    } catch (Exception e1) {
        // TODO Auto-generated catch block
        e1.printStackTrace();
    }
    String server = null;
    String username = null;
    String password = null;
    if (new File("mail.properties").exists()) {
        Properties properties = new Properties();
        try {
            properties.load(new FileInputStream(new File("mail.properties")));
            server = properties.getProperty("server");
            username = properties.getProperty("username");
            password = properties.getProperty("password");
            ArrayList<String> list = new ArrayList<String>(
                    Arrays.asList(new String[] { server, username, password }));
            list.addAll(Arrays.asList(args));
            args = list.toArray(new String[list.size()]);
        } catch (FileNotFoundException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        } catch (IOException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    if (args.length < 3) {
        System.err
                .println("Usage: POP3Mail <pop3 server hostname> <username> <password> [TLS [true=implicit]]");
        System.exit(1);
    }

    server = args[0];
    username = args[1];
    password = args[2];
    String proto = null;
    int messageid = -1;
    boolean implicit = false;
    for (int i = 3; i < args.length; ++i) {
        if (args[i].equals("-m")) {
            i += 1;
            messageid = Integer.parseInt(args[i]);
        }
    }

    // String proto = args.length > 3 ? args[3] : null;
    // boolean implicit = args.length > 4 ? Boolean.parseBoolean(args[4])
    // : false;

    POP3Client pop3;

    if (proto != null) {
        System.out.println("Using secure protocol: " + proto);
        pop3 = new POP3SClient(proto, implicit);
    } else {
        pop3 = new POP3Client();
    }
    pop3.setDefaultPort(110);
    System.out.println("Connecting to server " + server + " on " + pop3.getDefaultPort());

    // We want to timeout if a response takes longer than 60 seconds
    pop3.setDefaultTimeout(60000);
    // suppress login details
    pop3.addProtocolCommandListener(new PrintCommandListener(new PrintWriter(System.out), true));

    try {
        pop3.connect(server);
    } catch (IOException e) {
        System.err.println("Could not connect to server.");
        e.printStackTrace();
        System.exit(1);
    }

    try {
        if (!pop3.login(username, password)) {
            System.err.println("Could not login to server.  Check password.");
            pop3.disconnect();
            System.exit(1);
        }
        PrintWriter printWriter = new PrintWriter(new FileWriter("messages.csv"), true);
        POP3MessageInfo[] messages = null;
        POP3MessageInfo[] identifiers = null;
        if (messageid == -1) {
            messages = pop3.listMessages();
            identifiers = pop3.listUniqueIdentifiers();
        } else {
            messages = new POP3MessageInfo[] { pop3.listMessage(messageid) };
        }
        if (messages == null) {
            System.err.println("Could not retrieve message list.");
            pop3.disconnect();
            return;
        } else if (messages.length == 0) {
            System.out.println("No messages");
            pop3.logout();
            pop3.disconnect();
            return;
        }
        new File("../json").mkdirs();
        int count = 0;
        for (POP3MessageInfo msginfo : messages) {
            if (msginfo.number != identifiers[count].number) {
                throw new RuntimeException();
            }
            msginfo.identifier = identifiers[count].identifier;
            BufferedReader reader = (BufferedReader) pop3.retrieveMessageTop(msginfo.number, 0);
            ++count;
            if (count % 100 == 0) {
                logger.finest(String.format("%d %s", msginfo.number, msginfo.identifier));
            }
            System.out.println(String.format("%d %s", msginfo.number, msginfo.identifier));
            if (reader == null) {
                System.err.println("Could not retrieve message header.");
                pop3.disconnect();
                System.exit(1);
            }
            if (printMessageInfo(reader, msginfo.number, printWriter)) {
            }
        }
        printWriter.close();
        pop3.logout();
        pop3.disconnect();
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
}

From source file:PrintWriterDemo.java

public static void main() throws Exception {
    PrintWriter pw = new PrintWriter(new FileWriter("dice.txt"));
    for (int i = 1; i <= 1000; i++) {
        int die = (int) (1 + 6 * Math.random());
        pw.print(die);// ww  w. j  a  v  a 2  s  .c om
        pw.print(' ');
        if (i % 20 == 0)
            pw.println();
    }
    pw.println();
    pw.close(); // Without this, the output file may be empty
}

From source file:Main.java

private static void writeFileAsString(File file, String str) throws IOException {
    FileWriter fw = new FileWriter(file);
    fw.write(str);/*www.j a v a2 s.c  o  m*/
    fw.close();
}

From source file:Main.java

public static boolean putFileContent(File file, String content) throws IOException {
    FileWriter writer = new FileWriter(file);
    writer.write(content);/* www .  j av  a 2  s . c  om*/
    writer.flush();
    writer.close();
    return false;
}

From source file:Main.java

public static void writeJsonOnDisk(Context context, String fileName, StringBuilder bigStr) {
    try {//from w  w w. ja v a 2 s  .  c o m
        FileWriter Filewriter = new FileWriter(context.getApplicationInfo().dataDir + "/" + fileName + ".json");
        Filewriter.write(bigStr.toString());
        Filewriter.close();
    } catch (Exception e) {
        e.printStackTrace();
    }
}

From source file:Main.java

public static void writeFile(File file, String data) throws IOException {
    FileWriter fstream = new FileWriter(file);
    BufferedWriter out = new BufferedWriter(fstream);
    out.write(data);// ww  w  .j  av a 2  s.c  o  m
    out.close();
}

From source file:Main.java

public static String writeXMLToFile(String resString, String fileName) {
    try {/*  ww w . jav a  2  s.  c  om*/
        BufferedWriter writer = new BufferedWriter(new FileWriter(new File(fileName)));
        writer.write(resString);
        writer.close();
    } catch (IOException e) {
        e.printStackTrace();
        return null;
    }
    return fileName;
}

From source file:Main.java

public static void writeTextFile(File file, String text) {
    try {//  ww w .  j  a  v  a  2  s.  co m
        BufferedWriter bw = new BufferedWriter(new FileWriter(file));
        bw.write(text);
        bw.flush();
        bw.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

From source file:Main.java

public static boolean string2File(String res, File file) {
    if (file == null || res == null)
        return false;
    BufferedWriter bufferedWriter = null;
    try {// ww  w  . ja  v a  2 s. c  o  m
        bufferedWriter = new BufferedWriter(new FileWriter(file));
        bufferedWriter.write(res);
        bufferedWriter.flush();
        return true;
    } catch (IOException e) {
        e.printStackTrace();
        if (file.exists())
            file.delete();
        return false;
    } finally {
        try {
            if (bufferedWriter != null)
                bufferedWriter.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
}