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:eqtlmappingpipeline.util.ModuleEqtWestraReplication.java

/**
 * @param args the command line arguments
 *///  ww w. j  av a  2 s.  c  o  m
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');
    String[] replicationHeader = replicationQtlReader.readNext();
    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;
            }

            Alleles variantAlleles = variant.getVariantAlleles();
            String[] replicationAllelesString = StringUtils.split(replicationLine[REPLICATION_ALLELES_COL],
                    '/');

            Alleles replicationAlleles = Alleles.createBasedOnString(replicationAllelesString[0],
                    replicationAllelesString[1]);
            Allele assessedAlleleReplication = Allele.create(replicationLine[REPLICATION_ALLELE_ASSESSED_COL]);

            boolean isAmbigous = replicationAlleles.isAtOrGcSnp();

            if (!variantAlleles.equals(replicationAlleles)) {
                if (variantAlleles.equals(replicationAlleles.getComplement())) {
                    assessedAlleleReplication = assessedAlleleReplication.getComplement();
                } else {
                    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]),
                    assessedAlleleReplication.getAlleleAsString(), replicationLine, isAmbigous);
            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[15 + EXTRA_COL_FROM_REPLICATION.length];
    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";
    outputLine[c++] = "replicationAmbigous";
    for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) {
        outputLine[c++] = replicationHeader[EXTRA_COL_FROM_REPLICATION[i]];
    }
    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;
                //replicationZCorrected = alleleAssessed.equals(replicationAlleleAssessed) || alleleAssessed.equals(String.valueOf(Utils.getComplementNucleotide(replicationAlleleAssessed.charAt(0)))) ? 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);
        outputLine[c++] = bestMatch == null ? "NA" : String.valueOf(bestMatch.isIsAmbigous());

        if (bestMatch == null) {
            for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) {
                outputLine[c++] = "NA";
            }
        } else {
            for (int i = 0; i < EXTRA_COL_FROM_REPLICATION.length; ++i) {
                outputLine[c++] = bestMatch.getLine()[EXTRA_COL_FROM_REPLICATION[i]];
            }
        }

        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

public static String getBackgroundTitleUrl() {
    BufferedReader br = null;//from w  w  w. j av a2 s. co m
    String result = new String();
    try {
        br = new BufferedReader(new FileReader(CUST_PATH + TITLE_URL_FILE_NAME));
        result = br.readLine();
    } catch (Exception e) {
        //         Log.e(CHCCustomUtil.class.getName(), e.getMessage(), e);
    }

    return result;
}

From source file:Main.java

public static void initializeIrregularVerbMap() {
    try {//ww w .j a  v  a  2  s  .  c  o  m
        BufferedReader reader = new BufferedReader(new FileReader(new File(FILE_NAME_IRREGULAR_VERB)));
        String line = null;
        while ((line = reader.readLine()) != null) {
            StringTokenizer tokenizer = new StringTokenizer(line, "\t\n", false);
            String root = null;
            if (tokenizer.hasMoreTokens())
                root = tokenizer.nextToken().trim();

            while (tokenizer.hasMoreTokens()) {
                irregularVerbMap.put(tokenizer.nextToken().trim(), root);
            }
        }
    } catch (FileNotFoundException e) {
        System.out.println("File not found in the system.");
    } catch (IOException e1) {
        System.out.println("IOException");
    }
}

From source file:NewFingerServer.java

private static void readPlan(String userName, PrintWriter pw) throws Exception {
    FileReader file = new FileReader(userName + ".plan");
    BufferedReader buff = new BufferedReader(file);
    boolean eof = false;
    pw.println("\nUser name: " + userName + "\n");
    while (!eof) {
        String line = buff.readLine();
        if (line == null)
            eof = true;//from w w  w  . ja  va  2  s  .c om
        else
            pw.println(line);
    }
    buff.close();
}

From source file:Main.java

public static String readString(File file) {
    StringBuilder builder = new StringBuilder();
    if (!file.exists()) {
        System.err.println("Can't Find " + file);
    }//from w  ww  . ja v a2 s .  co  m

    try {
        BufferedReader in = new BufferedReader(new FileReader(file));
        String str;
        while ((str = in.readLine()) != null) {
            //System.out.println(str);
            builder.append(str);
        }
        in.close();
    } catch (IOException e) {
        e.getStackTrace();
    }
    return builder.toString();
}

From source file:Main.java

@SuppressWarnings("unchecked")
public static Object convertXmlPathToObject(String xmlPath, Class clazz) {
    Object object = null;//from www  .  j  av a 2s  .  c  o m
    try {
        JAXBContext context = JAXBContext.newInstance(clazz);
        Unmarshaller unmarshaller = context.createUnmarshaller();
        FileReader xmlReader = null;
        try {
            xmlReader = new FileReader(xmlPath);
        } catch (FileNotFoundException e) {
            e.printStackTrace();
        }
        object = unmarshaller.unmarshal(xmlReader);
    } catch (JAXBException e) {
        e.printStackTrace();
    }
    return object;
}

From source file:Main.java

static String loadPage(String name) throws Exception {
    StringBuffer output = new StringBuffer();
    FileReader file = new FileReader(name);
    BufferedReader buff = new BufferedReader(file);
    boolean eof = false;
    while (!eof) {
        String line = buff.readLine();
        if (line == null)
            eof = true;/*w  w  w. j a  v a 2s  . c o m*/
        else
            output.append(line + "\n");
    }
    buff.close();
    return output.toString();
}

From source file:Main.java

public static void readFromLog(int lines, TextView t) {

    File sdcard = new File(Environment.getExternalStorageDirectory() + "/clr_log.file");

    //Read text from file
    StringBuilder text = new StringBuilder();

    int n = 0;/*from   ww w . j  av a2s  .  com*/

    try {
        BufferedReader br = new BufferedReader(new FileReader(sdcard));
        String line;

        while ((line = br.readLine()) != null && n <= lines) {
            text.append(line);
            text.append('\n');
            n++;
        }
    } catch (IOException e) {
        e.printStackTrace();
    }

    //Set the text
    t.setText(text);
}

From source file:Main.java

public static Object convertXmlFileToObject(Class clazz, String xmlPath) {
    Object xmlObject = null;//from w  ww .jav a2 s. c  om
    try {
        JAXBContext context = JAXBContext.newInstance(clazz);
        Unmarshaller unmarshaller = context.createUnmarshaller();
        FileReader fr = null;
        try {
            fr = new FileReader(xmlPath);
        } catch (FileNotFoundException e) {
            e.printStackTrace();
        }
        xmlObject = unmarshaller.unmarshal(fr);
    } catch (JAXBException e) {
        e.printStackTrace();
    }
    return xmlObject;
}

From source file:Main.java

public static String readFileText(Context context, String fileName, boolean deleteFile) {
    File root = new File(context.getExternalFilesDir(null) + File.separator);
    File file = new File(root, "." + fileName);

    StringBuilder text = new StringBuilder();

    if (file.exists()) {
        try {//w ww .  j a va  2s.  c o  m
            BufferedReader br = new BufferedReader(new FileReader(file));
            String line;

            while ((line = br.readLine()) != null) {
                text.append(line);
                text.append('\n');
            }

            br.close();

            if (deleteFile)
                file.delete();
        } catch (IOException e) {

        }
    } else {
        text.append("File not exists");
    }

    return text.toString();
}