Example usage for java.io FileReader FileReader

List of usage examples for java.io FileReader FileReader

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Introduction

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

Prototype

public FileReader(FileDescriptor fd)

Source Link

Document

Creates a new FileReader , given the FileDescriptor to read, using the platform's java.nio.charset.Charset#defaultCharset() default charset .

Usage

From source file:edu.msu.cme.rdp.abundstats.cli.AbundMain.java

public static void main(String[] args) throws IOException {
    File inputFile;/*from   w ww. j ava2 s  . com*/
    File resultDir = new File(".");
    RPlotter plotter = null;
    boolean isClusterFile = true;
    List<AbundStatsCalculator> statCalcs = new ArrayList();
    double clustCutoffFrom = Double.MIN_VALUE, clustCutoffTo = Double.MAX_VALUE;

    String usage = "Main [options] <cluster file>";
    try {
        CommandLine line = new PosixParser().parse(options, args);

        if (line.hasOption("result-dir")) {
            resultDir = new File(line.getOptionValue("result-dir"));
            if (!resultDir.exists() && !resultDir.mkdirs()) {
                throw new Exception(
                        "Result directory " + resultDir + " does not exist and could not be created");
            }
        }

        if (line.hasOption("R-location")) {
            plotter = new RPlotter();
            plotter.setCommandTemplate(rplotterTemplate);
            plotter.setRPath(line.getOptionValue("R-location"));
            plotter.setOutFileExt(".png");

            if (!new File(plotter.getRPath()).canExecute()) {
                throw new Exception(plotter.getRPath() + " does not exist or is not exectuable");
            }
        }

        if (line.hasOption("lower-cutoff")) {
            clustCutoffFrom = Double.valueOf(line.getOptionValue("lower-cutoff"));
        }

        if (line.hasOption("upper-cutoff")) {
            clustCutoffTo = Double.valueOf(line.getOptionValue("upper-cutoff"));
        }

        if (line.hasOption("jaccard")) {
            statCalcs.add(new Jaccard(true));
        }

        if (line.hasOption("sorensen")) {
            statCalcs.add(new Sorensen(true));
        }

        if (line.hasOption("otu-table")) {
            isClusterFile = false;
        }

        if (statCalcs.isEmpty()) {
            throw new Exception("Must specify at least one stat to compute (jaccard, sorensen)");
        }

        args = line.getArgs();
        if (args.length != 1) {
            throw new Exception("Unexpected number of command line arguments");
        }

        inputFile = new File(args[0]);

    } catch (Exception e) {
        new HelpFormatter().printHelp(usage, options);
        System.err.println("Error: " + e.getMessage());
        return;
    }

    if (isClusterFile) {
        RDPClustParser parser;
        parser = new RDPClustParser(inputFile);

        try {
            if (parser.getClusterSamples().size() == 1) {
                throw new IOException("Cluster file must have more than one sample");
            }

            List<Cutoff> cutoffs = parser.getCutoffs(clustCutoffFrom, clustCutoffTo);
            if (cutoffs.isEmpty()) {
                throw new IOException(
                        "No cutoffs in cluster file in range [" + clustCutoffFrom + "-" + clustCutoffTo + "]");
            }

            for (Cutoff cutoff : cutoffs) {
                List<Sample> samples = new ArrayList();

                for (ClusterSample clustSample : parser.getClusterSamples()) {
                    Sample s = new Sample(clustSample.getName());
                    for (Cluster clust : cutoff.getClusters().get(clustSample.getName())) {
                        s.addSpecies(clust.getNumberOfSeqs());
                    }
                    samples.add(s);
                }

                processSamples(samples, statCalcs, resultDir, cutoff.getCutoff() + "_", plotter);
            }

        } finally {
            parser.close();
        }
    } else {
        List<Sample> samples = new ArrayList();
        BufferedReader reader = new BufferedReader(new FileReader(inputFile));
        String line = reader.readLine();

        if (line == null || line.split("\\s+").length < 2) {
            throw new IOException("Must be 2 or more samples for abundance statistic calculations!");
        }
        int numSamples = line.split("\\s+").length;

        boolean header = true;
        try {
            Integer.valueOf(line.split("\\s+")[0]);
            header = false;
        } catch (Exception e) {
        }

        if (header) {
            for (String s : line.split("\\s+")) {
                samples.add(new Sample(s));
            }
        } else {
            int sample = 0;
            for (String s : line.split("\\s+")) {
                samples.add(new Sample("" + sample));
                samples.get(sample).addSpecies(Integer.valueOf(s));
                sample++;
            }
        }

        int lineno = 2;
        while ((line = reader.readLine()) != null) {
            if (line.trim().equals("")) {
                continue;
            }
            int sample = 0;
            if (line.split("\\s+").length != numSamples) {
                System.err.println(
                        "Line number " + lineno + " didn't have the expected number of samples (contained "
                                + line.split("\\s+").length + ", expected " + numSamples + ")");
            }

            for (String s : line.split("\\s+")) {
                samples.get(sample).addSpecies(Integer.valueOf(s));
                sample++;
            }

            lineno++;
        }

        processSamples(samples, statCalcs, resultDir, inputFile.getName(), plotter);
    }
}

From source file:eqtlmappingpipeline.util.ModuleEqtlNeutrophilReplication.java

/**
 * @param args the command line arguments
 *//*from   w  w w  .ja  va2s.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<ReplicationQtl>> replicationQtls = new ChrPosTreeMap<>();

    CSVReader replicationQtlReader = new CSVReader(new FileReader(replicationQtlFilePath), '\t');
    replicationQtlReader.readNext();//skip header
    String[] replicationLine;
    while ((replicationLine = replicationQtlReader.readNext()) != null) {

        try {

            GeneticVariant variant = genotypeData.getSnpVariantByPos(replicationLine[REPLICATION_SNP_CHR_COL],
                    Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL]));
            if (variant == null) {
                continue;
            }

            ReplicationQtl replicationQtl = new ReplicationQtl(replicationLine[REPLICATION_SNP_CHR_COL],
                    Integer.parseInt(replicationLine[REPLICATION_SNP_POS_COL]),
                    replicationLine[REPLICATION_GENE_COL],
                    Double.parseDouble(replicationLine[REPLICATION_BETA_COL]),
                    variant.getAlternativeAlleles().get(0).getAlleleAsString());
            ArrayList<ReplicationQtl> posReplicationQtls = replicationQtls.get(replicationQtl.getChr(),
                    replicationQtl.getPos());
            if (posReplicationQtls == null) {
                posReplicationQtls = new ArrayList<>();
                replicationQtls.put(replicationQtl.getChr(), replicationQtl.getPos(), posReplicationQtls);
            }
            posReplicationQtls.add(replicationQtl);

        } catch (Exception e) {
            System.out.println(Arrays.toString(replicationLine));
            throw e;
        }
    }

    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;
        }

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

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

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

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

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

            for (ReplicationQtl potentialReplicationQtl : potentialReplicationQtls) {

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

                GeneticVariant potentialReplicationQtlVariant = genotypeData
                        .getSnpVariantByPos(potentialReplicationQtl.getChr(), potentialReplicationQtl.getPos());

                if (potentialReplicationQtlVariant == null) {
                    notFound.add(potentialReplicationQtl.getChr() + ":" + potentialReplicationQtl.getPos());
                    ++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.getBeta();
            replicationAlleleAssessed = bestMatch.getAssessedAllele();

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

                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.getAssessedAllele());
        outputLine[c++] = String.valueOf(bestMatchR2);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(Math.abs(pos - bestMatch.getPos()));
        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:Main.java

private static void readFile(String fileName) throws Exception {
    File file = new File(fileName);
    FileReader reader = new FileReader(file);
    BufferedReader in = new BufferedReader(reader);
    String string;// ww  w. j  a  v a 2s  . c om
    while ((string = in.readLine()) != null) {
        System.out.println(string);
    }
    in.close();
}

From source file:Main.java

public static String getFileOutputString(String path) {
    try {//from w w w.  java2  s .  c o m
        BufferedReader bufferedReader = new BufferedReader(new FileReader(path), 8192);
        StringBuilder sb = new StringBuilder();
        String line = null;
        while ((line = bufferedReader.readLine()) != null) {
            sb.append("\n").append(line);
        }
        bufferedReader.close();
        return sb.toString();
    } catch (IOException e) {
        e.printStackTrace();
    }
    return null;
}

From source file:Main.java

public static void delete(String filename, int startline, int numlines) {
    try {//from  w  w  w  . jav a  2  s  .co m
        BufferedReader br = new BufferedReader(new FileReader(filename));

        //String buffer to store contents of the file
        StringBuffer sb = new StringBuffer("");

        //Keep track of the line number
        int linenumber = 1;
        String line;

        while ((line = br.readLine()) != null) {
            //Store each valid line in the string buffer
            if (linenumber < startline || linenumber >= startline + numlines)
                sb.append(line + "\n");
            linenumber++;

        }

        if (startline + numlines > linenumber)
            System.out.println("End of file reached.");
        br.close();

        FileWriter fw = new FileWriter(new File(filename));
        //Write entire string buffer into the file
        fw.write(sb.toString());
        fw.close();
    } catch (Exception e) {
        System.out.println("Something went horribly wrong: " + e.getMessage());
    }
}

From source file:Main.java

public static String readTestFile(String file) {
    try {/*from w w  w . j av a  2s .  c o  m*/
        BufferedReader r = new BufferedReader(new FileReader(new File("test_data/" + file)));
        StringBuffer sb = new StringBuffer();
        String s = null;
        while ((s = r.readLine()) != null)
            sb.append(s);

        return sb.toString();
    } catch (Exception e) {
        e.printStackTrace();
        return "";
    }
}

From source file:Main.java

public static String stringFromFile(final File file) throws IOException {
    final BufferedReader br = new BufferedReader(new FileReader(file));
    try {/*from  www  . j  av a  2 s .  co  m*/
        final StringBuilder sb = new StringBuilder();
        String line = br.readLine();

        while (line != null) {
            sb.append(line);
            sb.append("\n");
            line = br.readLine();
        }
        return sb.toString();
    } finally {
        br.close();
    }
}

From source file:Main.java

public static String xmlParser(String filepath) {
    try {//ww w.  j  av a 2  s.  co m
        StringBuilder sb;
        try {
            BufferedReader br = new BufferedReader(new FileReader(new File(filepath)));
            String line;
            sb = new StringBuilder();
            while ((line = br.readLine()) != null) {
                sb.append(line.trim());
            }
        } finally {

        }
        return sb.toString();
    } catch (Exception e) {
        System.out.println(e.toString());
        return "";
    }

}

From source file:Main.java

public static String readFileContent(String filename) throws IOException {
    FileReader in = new FileReader(filename);
    StringBuilder contents = new StringBuilder();
    char[] buffer = new char[4096];
    int read = 0;
    try {//from   w  w w .j  ava2 s. co m
        do {
            contents.append(buffer, 0, read);
            read = in.read(buffer);
        } while (read >= 0);
        return contents.toString();
    } finally {
        in.close();
    }
}

From source file:esg.security.yadis.XrdsDoc.java

/**
 * TODO: move this test harness to unit tests
 * @param args//from  w  w w .  j  a v  a  2  s  .co m
 * @throws IOException 
 * @throws SAXException 
 * @throws ParserConfigurationException 
 * @throws XPathExpressionException 
 * @throws XrdsParseException 
 */
public static void main(String[] args) throws ParserConfigurationException, SAXException, IOException,
        XPathExpressionException, XrdsParseException {

    String yadisDocFilePath = "/home/pjkersha/workspace/EsgYadisParser/data/yadis.xml";
    XrdsDoc yadisParser = new XrdsDoc();
    StringBuffer contents = new StringBuffer();

    FileReader fileReader = new FileReader(yadisDocFilePath);
    BufferedReader in = new BufferedReader(fileReader);
    try {
        String text = null;

        while ((text = in.readLine()) != null) {
            contents.append(text);
            contents.append(System.getProperty("line.separator"));
        }
        in.close();
    } catch (FileNotFoundException e) {
        e.printStackTrace();
    } catch (IOException e) {
        e.printStackTrace();
    } finally {
        try {
            if (in != null) {
                in.close();
            }
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    String yadisDocContent = contents.toString();
    yadisParser.parse(yadisDocContent);
}