Example usage for org.apache.commons.io FileUtils writeLines

Introduction

In this page you can find the example usage for org.apache.commons.io FileUtils writeLines.

Prototype

public static void writeLines(File file, Collection lines) throws IOException 

Source Link

Document

Writes the toString() value of each item in a collection to the specified File line by line.

Usage

From source file:specminers.evaluation.ValidSpecGenerator.java

private static void extractInvalidSequences(Map<String, String> options) throws IOException, ParseException {
    File mopFilesFolder = new File(options.get(INPUT_PATH_OPTION));
    String[] extensions = new String[] { MopExtractor.MOP_FILES_EXTENSION };
    List<File> files = FileUtils.listFiles(mopFilesFolder, extensions, true).stream()
            .collect(Collectors.toList());

    List<String> forbiddenSequences = new LinkedList<>();

    for (File f : files) {
        MopExtractor extractor = new MopExtractor(f);

        if (extractor.containsParseableSpec()) {
            forbiddenSequences.addAll(extractor.getForbiddenSequences());
        }//  www.  j av a 2 s .  c om
    }

    File outputDir = new File(options.get(OUTPUT_OPTION));

    if (outputDir == null || !outputDir.exists()) {
        forbiddenSequences.forEach(l -> System.out.println(l));
    } else {
        File forbiddenSeqsFile;
        forbiddenSeqsFile = java.nio.file.Paths.get(outputDir.getAbsolutePath(), "forbidden_sequences.txt")
                .toFile();
        FileUtils.writeLines(forbiddenSeqsFile, forbiddenSequences);

    }
}

---

From source file:trigeditor.editors.PrefixRefactor.java

/**
 * Function that refactors prefixes. For URIs that haven't been matched to a prefix yet
 * and appear in the file at least 5 times, this function adds the prefix name and URI 
 * to the top of the list of prefixes in the file. In addition, all occurrences of the URI
 * are replaced by the prefix name. If there is additional text in the URI, the text is 
 * separated by ':' from the prefix name.
 * //ww  w  . j ava 2 s  . com
 * Additionally, the same URI should not appear multiple times in a triple statement.
 * 
 * @param input String representation of the file whose prefixes are being refactored.
 * @param fileName String representation of the path of the file
 * @throws IOException
 */
public void refactorPrefixes(String input, String filePath) throws IOException {
    File f = new File(filePath);

    //prevent concurrency issues: using different data structures to avoid access/changing at same time
    List<String> lines = FileUtils.readLines(f);
    List<String> tempLines = new ArrayList<String>();
    List<String> tempLinesRename = new ArrayList<String>();

    Map<String, String> tempPrefixes = new HashMap<String, String>();
    Map<String, String> tempURIRename = new HashMap<String, String>();
    tempPrefixes = generatePrefixes(input);
    tempURIRename = generatePrefixes(input);

    //Add prefix name to list of prefixes
    int index = 1;
    for (String s : lines) {
        tempLines.add(s);
        if (s.contains("@prefix") && !tempPrefixes.isEmpty()) {
            for (String URI : tempPrefixes.keySet()) {
                tempLines.add(index - 1, "@prefix " + tempPrefixes.get(URI) + "   :   " + "<" + URI + "> .");
                tempPrefixes.remove(URI);
            }
        }

        index++;
    }
    //case where there are no prefixes listed in the file
    if (!tempPrefixes.isEmpty()) {
        for (String URI : tempPrefixes.keySet()) {
            tempLines.add(0, "@prefix " + tempPrefixes.get(URI) + "   :   " + "<" + URI + "> .");
            tempPrefixes.remove(URI);
        }
    }

    //Replace URIs with prefix name in document
    int index2 = 0;
    for (String s : tempLines) {
        tempLinesRename.add(s);
        for (String uri : tempURIRename.keySet()) {
            String strAtLine = tempLinesRename.get(index2);
            if (strAtLine.contains(uri) && !strAtLine.contains("@prefix")) {
                int start = strAtLine.indexOf(uri) + uri.length();
                String strAtLineNew = "";
                if (start > 0) {
                    int i = start;
                    String temp = strAtLine;
                    if (strAtLine.charAt(start) == '#' || strAtLine.charAt(start) == '/') {
                        temp = strAtLine.substring(0, start) + ":" + strAtLine.substring(start + 1);
                    }
                    while (temp.charAt(i) != '>') {
                        i++;
                    }

                    if (i != temp.length() - 1) {
                        strAtLineNew = temp.substring(0, i) + temp.substring(i + 1);
                    } else {
                        strAtLineNew = temp.substring(0, i);
                    }
                }

                CharSequence target = "<" + uri;
                CharSequence literal = tempURIRename.get(uri);
                tempLinesRename.set(index2, strAtLineNew.replace(target, literal));

            }
        }
        index2++;
    }

    FileUtils.writeLines(f, tempLinesRename);
}

---

From source file:uk.ac.tgac.citadel.CitadelCLI.java

public void execute() throws InterruptedException, TaskExecutionException, IOException {

    // Run the pipeline as described by the user
    TaskResult result = super.execute(new GuestUser("citadel@tgac.ac.uk"), ConanTask.Priority.HIGH,
            this.executionContext);

    // Output the resource usage to file
    FileUtils.writeLines(new File(this.args.getOutputDir(), this.args.getJobPrefix() + ".summary"),
            result.getOutput());/*from w  w  w  .ja  v  a 2  s. co  m*/
}

---

From source file:uk.ac.tgac.conan.process.asm.tools.AllpathsLgV50.java

protected void createPloidyFile(int ploidy, File ploidyFile) throws IOException {

    List<String> lines = new ArrayList<>();
    lines.add(Integer.toString(ploidy));

    FileUtils.writeLines(ploidyFile, lines);
}

---

From source file:uk.ac.tgac.conan.process.asm.tools.AllpathsLgV50.java

protected void createLibFile(File libFile, List<Library> libraries) throws IOException {

    List<String> lines = new ArrayList<String>();

    lines.add(/*from   w  w w.j  av  a  2 s  .  c o m*/
            "library_name, project_name, organism_name, type, paired, frag_size, frag_stddev, insert_size, insert_stddev, read_orientation, genomic_start, genomic_end");

    for (Library lib : libraries) {

        String type = "";
        String paired = "";
        String fragSize = "";
        String fragDev = "";
        String insertSize = "";
        String insertDev = "";
        String readOrientation = "";

        switch (lib.getType()) {
        case OPE:
            type = "fragment";
            paired = "1";
            fragSize = Integer.toString(lib.getAverageInsertSize());
            fragDev = Integer.toString((int) (lib.getAverageInsertSize() * lib.getInsertErrorTolerance()));
            readOrientation = lib.getSeqOrientation() == Library.SeqOrientation.FR ? "inward" : "outward";
            break;
        case PE:
            type = "jumping";
            paired = "1";
            insertSize = Integer.toString(lib.getAverageInsertSize());
            insertDev = Integer.toString((int) (lib.getAverageInsertSize() * lib.getInsertErrorTolerance()));
            readOrientation = lib.getSeqOrientation() == Library.SeqOrientation.FR ? "inward" : "outward";
            break;
        case MP:
            type = "long_jump";
            paired = "1";
            insertSize = Integer.toString(lib.getAverageInsertSize());
            insertDev = Integer.toString((int) (lib.getAverageInsertSize() * lib.getInsertErrorTolerance()));
            readOrientation = lib.getSeqOrientation() == Library.SeqOrientation.FR ? "inward" : "outward";
            break;
        case SE:
            type = "long";
            paired = "0";
            break;
        }

        List<String> parts = new ArrayList<String>();
        parts.add(lib.getName());
        parts.add("rampart");
        parts.add(this.getArgs().getOrganism().getName().replaceAll(" ", "_"));
        parts.add(type);
        parts.add(paired);
        parts.add(fragSize);
        parts.add(fragDev);
        parts.add(insertSize);
        parts.add(insertDev);
        parts.add(readOrientation);
        parts.add("");
        parts.add("");

        lines.add(StringUtils.join(parts, ", "));
    }

    FileUtils.writeLines(libFile, lines);
}

---

From source file:uk.ac.tgac.conan.process.asm.tools.AllpathsLgV50.java

private GroupInfo createGroupFiles(List<Library> libraries) throws IOException {

    int countOpe = 0;
    int countPe = 0;
    int countMp = 0;
    int countLong = 0;

    List<String> phred33Lines = new ArrayList<>();
    List<String> phred64Lines = new ArrayList<>();
    List<String> groupNames = new ArrayList<>();

    final String groupHeader = "group_name, library_name, file_name";

    phred33Lines.add(groupHeader);/*from  w ww  .j a  va 2s .com*/
    phred64Lines.add(groupHeader);

    for (Library lib : libraries) {

        String groupName = lib.getType().toString();

        switch (lib.getType()) {
        case OPE:
            countOpe++;
            groupName += countOpe;
            break;
        case PE:
            countPe++;
            groupName += countPe;
            break;
        case MP:
            countMp++;
            groupName += countMp;
            break;
        case SE:
            countLong++;
            groupName += countLong;
            break;
        default:
        }

        groupNames.add(groupName);

        List<String> parts = new ArrayList<String>();
        parts.add(groupName);
        parts.add(lib.getName());

        if (lib.getType() == Library.Type.SE) {
            parts.add(lib.getFile1().getAbsolutePath());
        } else {
            parts.add(createGlobPattern(lib.getFile1(), lib.getFile2()));
        }

        String groupLine = StringUtils.join(parts, ", ");

        if (lib.getPhred() == null || lib.getPhred() == Library.Phred.PHRED_64) {
            phred64Lines.add(groupLine);
        } else {
            phred33Lines.add(groupLine);
        }

    }

    File p33File = null;
    File p64File = null;
    File outputDir = this.getArgs().getOutputDir();

    if (phred33Lines.size() > 1) {
        p33File = new File(outputDir, "in_groups_phred33.csv");
        FileUtils.writeLines(p33File, phred33Lines);
    }

    if (phred64Lines.size() > 1) {
        p64File = new File(outputDir, "in_groups_phred64.csv");
        FileUtils.writeLines(p64File, phred64Lines);
    }

    return new GroupInfo(p33File, p64File, groupNames);
}

---

From source file:uk.ac.tgac.conan.process.re.tools.QuakeV03.java

@Override
public void setup() {
    String pwdFull = new File(".").getAbsolutePath();
    String pwd = pwdFull.substring(0, pwdFull.length() - 2);

    this.addPreCommand("cd " + this.getArgs().getOutputDir().getAbsolutePath());
    this.addPostCommand("cd " + pwd);

    Args args = this.getArgs();

    if (args.getReadsListFile() == null || !args.getReadsListFile().exists()) {

        if (args.getInput() == null) {
            throw new IllegalArgumentException(
                    "Input reads file does not exist and no library object provided.  Cannot continue.");
        }/*  www.j  a v a 2 s  .  co m*/

        final ConanProcessService cps = this.conanExecutorService.getConanProcessService();

        boolean pairedEnd = args.getInput().isPairedEnd();

        File in1 = new File(args.getOutputDir(), args.getInput().getFile1().getName());
        File in2 = pairedEnd ? new File(args.getOutputDir(), args.getInput().getFile2().getName()) : null;

        try {
            cps.createLocalSymbolicLink(args.getInput().getFile1(), in1);
            if (pairedEnd) {
                cps.createLocalSymbolicLink(args.getInput().getFile2(), in2);
            }
        } catch (ProcessExecutionException | InterruptedException e) {
            throw new IllegalArgumentException("Could not create symbolic links for input files.", e);
        }

        String fp1 = in1.getAbsolutePath();
        String fp2 = pairedEnd ? " " + in2.getAbsolutePath() : "";

        String outLine = fp1 + fp2;

        List<String> outLines = new ArrayList<>();
        outLines.add(outLine);

        File inputFileList = new File(args.getOutputDir(), "readsListFile.lst");
        args.setReadsListFile(inputFileList);
        args.setQualityScale(args.getInput().getPhred() == null ? 0
                : args.getInput().getPhred() == Library.Phred.PHRED_33 ? 33 : 64);

        try {
            FileUtils.writeLines(inputFileList, outLines);
        } catch (IOException e) {
            throw new IllegalArgumentException(
                    "Could not output Quake reads configuration file: " + inputFileList, e);
        }
    }
}

---

From source file:uk.ac.tgac.jellyswarm.StatsProcess.java

protected void createStatsFile(List<File> statsFiles, File outputFile) throws IOException {

    List<String> outputLines = new ArrayList<>();

    // Add header
    outputLines.add("filename\tunique\tdistinct\ttotal\tmax_count");

    for (File file : statsFiles) {

        List<String> statsLines = FileUtils.readLines(file);

        long unique = 0;
        long distinct = 0;
        long total = 0;
        long maxCount = 0;

        for (String line : statsLines) {
            if (line.startsWith("Unique")) {
                String[] parts = line.split("\\s+");
                unique = Long.parseLong(parts[1]);
            }/*w  w  w  .  j  ava  2 s.c o m*/
            if (line.startsWith("Distinct")) {
                String[] parts = line.split("\\s+");
                distinct = Long.parseLong(parts[1]);
            }
            if (line.startsWith("Total")) {
                String[] parts = line.split("\\s+");
                total = Long.parseLong(parts[1]);
            }
            if (line.startsWith("Max_count")) {
                String[] parts = line.split("\\s+");
                maxCount = Long.parseLong(parts[1]);
            }
        }

        StringBuilder sb = new StringBuilder();

        sb.append(file.getName()).append("\t").append(unique).append("\t").append(distinct).append("\t")
                .append(total).append("\t").append(maxCount);

        outputLines.add(sb.toString());
    }

    FileUtils.writeLines(outputFile, outputLines);
}

---

From source file:uk.ac.tgac.jellyswarm.StatsProcess.java

private void createDistinctStatsFile(List<File> statsFiles, File outputFile) throws IOException {

    List<String> lines = new ArrayList<>();

    lines.add("filename\tmin\tmax\tmean\tvariance\tstddev");

    for (File file : statsFiles) {

        long min = Long.MAX_VALUE;
        long max = 0;
        long sum = 0;
        long sum2 = 0;

        List<String> statsLines = FileUtils.readLines(file);

        for (int i = 1; i < statsLines.size(); i++) {

            String line = statsLines.get(i);

            String[] parts = line.split("\t");

            long distinctVal = Long.parseLong(parts[2]);

            min = distinctVal < min ? distinctVal : min;
            max = distinctVal > max ? distinctVal : max;

            sum += distinctVal;//ww  w  .  j  a v a  2 s  .  c o m
            sum2 += distinctVal * distinctVal;
        }

        int entries = statsLines.size() - 1;
        double mean = (double) sum / (double) entries;
        double var = ((sum * sum) - sum2) / (double) entries;
        double stddev = Math.sqrt(var);

        lines.add(file.getName() + "\t" + min + "\t" + max + "\t" + mean + "\t" + var + "\t" + stddev);
    }

    FileUtils.writeLines(outputFile, lines);
}

---

From source file:uk.ac.tgac.rampart.RampartCLI.java

public void execute() throws InterruptedException, TaskExecutionException, IOException {

    // Run the pipeline as described by the user
    TaskResult result = super.execute(new GuestUser("rampart@tgac.ac.uk"), ConanTask.Priority.HIGH,
            this.args.getExecutionContext());

    // Output the resource usage to file
    FileUtils.writeLines(new File(this.args.getOutputDir(), this.args.getJobPrefix() + ".summary"),
            result.getOutput());/* www.  jav  a2 s .  c  o  m*/
}

---

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