List of usage examples for java.nio.file Files newBufferedWriter
public static BufferedWriter newBufferedWriter(Path path, OpenOption... options) throws IOException
From source file:org.duracloud.snapshot.service.impl.SpaceItemWriterTest.java
private BufferedWriter createWriter(File contentDir, String name) throws IOException { Path propsPath = ContentDirUtils.getPath(contentDir, name); BufferedWriter propsWriter = Files.newBufferedWriter(propsPath, StandardCharsets.UTF_8); return propsWriter; }
From source file:popgenutils.dfcp.PrepareVCF4DFCP.java
/** * /* w ww . ja va 2 s . c o m*/ */ private void makegeno() { gt_string_builder = new StringBuilder(); StringBuilder header = new StringBuilder(); try (BufferedReader in = Files.newBufferedReader(Paths.get(filename), Charset.forName("UTF-8"))) { BufferedWriter out = null; BufferedWriter out_bgl_ref = null; BufferedWriter out_bgl_geno = null; String line = null; int number_of_individuals = 0; Set<Integer> individuals_to_genotype = new HashSet<Integer>(); while ((line = in.readLine()) != null) { if (line.startsWith("#CHROM")) { StringBuilder bglref_header = new StringBuilder(); StringBuilder bglgeno_header = new StringBuilder(); String[] parts = line.split("\t"); //samples begin at 9 number_of_individuals = parts.length - 9; List<Integer> index_of_individuals = new ArrayList<Integer>(); for (int i = 0; i < number_of_individuals; i++) { index_of_individuals.add(i); } Collections.shuffle(index_of_individuals); if (pgeno >= 0) { // convert pgeno into ageno ageno = (int) Math.ceil(number_of_individuals * pgeno); } for (int i = 0; i < ageno; i++) { individuals_to_genotype.add(index_of_individuals.get(i)); } bglref_header.append(parts[0]); bglgeno_header.append(parts[0]); for (int i = 1; i < 9; i++) { bglref_header.append("\t" + parts[i]); bglgeno_header.append("\t" + parts[i]); } for (int i = 9; i < parts.length; i++) { int index = i - 9; if (individuals_to_genotype.contains(index)) { bglgeno_header.append("\t" + parts[i]); } else { bglref_header.append("\t" + parts[i]); } } out = Files.newBufferedWriter( Paths.get(output_dir + "/" + ageno + "_geno" + Paths.get(filename).getFileName()), Charset.forName("UTF-8")); out_bgl_ref = Files.newBufferedWriter( Paths.get( output_dir + "/" + ageno + "_geno_bglref" + Paths.get(filename).getFileName()), Charset.forName("UTF-8")); out_bgl_geno = Files.newBufferedWriter( Paths.get(output_dir + "/" + ageno + "_geno_bgl" + Paths.get(filename).getFileName()), Charset.forName("UTF-8")); out.write(header.toString()); out_bgl_ref.write(header.toString()); out_bgl_geno.write(header.toString()); out.write(line + System.getProperty("line.separator")); out_bgl_geno.write(bglgeno_header + System.getProperty("line.separator")); out_bgl_ref.write(bglref_header + System.getProperty("line.separator")); } else if (line.startsWith("#")) { header.append(line + System.getProperty("line.separator")); } else { // format at 8 String[] parts = line.split("\t"); String[] parts2 = parts[8].split(":"); int gt_pos = 0; for (int i = 1; i < parts2.length; i++) { if (parts2[i].equals("GT")) gt_pos = i; } out.write(parts[0]); out_bgl_geno.write(parts[0]); out_bgl_ref.write(parts[0]); for (int i = 1; i < parts.length; i++) { if (i > 8) { parts2 = parts[i].split(":"); if (gt_pos == 0 && individuals_to_genotype.contains(i - 9)) { out.write("\t" + convertToGT(parts2[0])); out_bgl_geno.write("\t" + convertToGT(parts2[0])); } else { out.write("\t" + parts2[0]); out_bgl_ref.write("\t" + parts2[0]); } for (int j = 1; j < parts2.length; j++) { if (gt_pos == j && individuals_to_genotype.contains(i - 9)) { out.write(":" + convertToGT(parts2[i])); out_bgl_geno.write(":" + convertToGT(parts2[i])); } else { out.write(":" + parts2[i]); out_bgl_ref.write(":" + parts2[i]); } } } else { out.write("\t" + parts[i]); out_bgl_ref.write("\t" + parts[i]); out_bgl_geno.write("\t" + parts[i]); } } out.write(System.getProperty("line.separator")); out_bgl_ref.write(System.getProperty("line.separator")); out_bgl_geno.write(System.getProperty("line.separator")); } } out.close(); out_bgl_ref.close(); out_bgl_geno.close(); } catch (IOException e) { System.err.println("could not read from file " + filename); e.printStackTrace(); } }
From source file:sadl.models.PDTTAold.java
public void toGraphvizFile(Path graphvizResult, boolean compressed) throws IOException { final BufferedWriter writer = Files.newBufferedWriter(graphvizResult, StandardCharsets.UTF_8); writer.write("digraph G {\n"); // start states writer.write("qi [shape = point ];"); // write states for (final int state : finalStateProbabilities.keys()) { writer.write(Integer.toString(state)); writer.write(" [shape="); final boolean abnormal = getFinalTransition(state).isAbnormal(); final double finalProb = getFinalStateProbability(state); if (finalProb > 0 || (compressed && finalProb > 0.01)) { writer.write("double"); }/*from w w w .j a v a 2s. co m*/ writer.write("circle"); if (abnormal) { writer.write(", color=red"); } if (finalProb > 0 || (compressed && finalProb > 0.01)) { writer.write(", label=\""); writer.write(Integer.toString(state)); writer.write("\np= "); writer.write(Double.toString(Precision.round(finalProb, 2))); writer.write("\""); } writer.write("];\n"); } writer.write("qi -> 0;"); // write transitions for (final Transition t : transitions) { if (compressed && t.getProbability() <= 0.01) { continue; } // 0 -> 0 [label=0.06]; writer.write(Integer.toString(t.getFromState())); writer.write(" -> "); writer.write(Integer.toString(t.getToState())); writer.write(" [label=<"); writer.write(t.getSymbol()); if (t.getProbability() > 0) { writer.write(" p="); writer.write(Double.toString(Precision.round(t.getProbability(), 2))); } if (t.isAbnormal()) { writer.write("<BR/>"); writer.write("<FONT COLOR=\"red\">"); writer.write(Integer.toString(t.getAnomalyInsertionType().getTypeIndex())); writer.write("</FONT>"); } writer.write(">"); if (t.isAbnormal()) { writer.write(" color=\"red\""); } writer.write(";];\n"); } writer.write("}"); writer.close(); }
From source file:sadl.models.PDFA.java
public void toGraphvizFile(Path graphvizResult, boolean compressed, Map<String, String> idReplacement) throws IOException { try (BufferedWriter writer = Files.newBufferedWriter(graphvizResult, StandardCharsets.UTF_8)) { writer.write("digraph G {\n"); // start states writer.write("qi [shape = point ];"); // write states for (final int state : finalStateProbabilities.keys()) { writer.write(Integer.toString(state)); writer.write(" [shape="); final boolean abnormal = getFinalTransition(state).isAbnormal(); final double finalProb = getFinalStateProbability(state); if (finalProb > 0 || (compressed && finalProb > 0.01)) { writer.write("double"); }//from w w w .j a v a 2 s . co m writer.write("circle"); if (abnormal) { writer.write(", color=red"); } if (finalProb > 0 || (compressed && finalProb > 0.01)) { writer.write(", label=\""); writer.write(Integer.toString(state)); writer.write("\np= "); writer.write(Double.toString(Precision.round(finalProb, 2))); writer.write("\""); } writer.write("];\n"); } writer.write("qi -> 0;"); // write transitions for (final Transition t : transitions) { if (compressed && t.getProbability() <= 0.01) { continue; } // 0 -> 0 [label=0.06]; writer.write(Integer.toString(t.getFromState())); writer.write(" -> "); writer.write(Integer.toString(t.getToState())); writer.write(" [label=<"); if (idReplacement != null && idReplacement.containsKey(t.getSymbol())) { writer.write(idReplacement.get(t.getSymbol())); } else { writer.write(t.getSymbol()); } if (t.getProbability() > 0) { writer.write(" p="); writer.write(Double.toString(Precision.round(t.getProbability(), 2))); } if (t.isAbnormal()) { writer.write("<BR/>"); writer.write("<FONT COLOR=\"red\">"); writer.write(Integer.toString(t.getAnomalyInsertionType().getTypeIndex())); writer.write("</FONT>"); } writer.write(">"); if (t.isAbnormal()) { writer.write(" color=\"red\""); } writer.write(";];\n"); } writer.write("}"); writer.flush(); writer.close(); } }
From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java
public boolean createCacheFileAntibioticResistanceGenes(String filePath) { boolean isSuccess = false; JSONObject jsonData = new JSONObject(); JSONObject data;/*from w w w. j a va 2 s . com*/ // from WP // data data = read(baseURL + "/tab/dlp-antibioticresistance-data/?req=passphrase"); if (data != null) { jsonData.put("data", data); } // popular genomes data = this.getPopularGenomesForAntibioticResistanceGene(); if (data != null) { jsonData.put("popularGenomes", data); } // tools data = read(baseURL + "/tab/dlp-antibioticresistance-tools/?req=passphrase"); if (data != null) { jsonData.put("tools", data); } // process data = read(baseURL + "/tab/dlp-antibioticresistance-process/?req=passphrase"); if (data != null) { jsonData.put("process", data); } // download data = read(baseURL + "/tab/dlp-antibioticresistance-download/?req=passphrase"); if (data != null) { jsonData.put("download", data); } // save jsonData to file try (PrintWriter jsonOut = new PrintWriter( Files.newBufferedWriter(FileSystems.getDefault().getPath(filePath), Charset.defaultCharset()));) { jsonData.writeJSONString(jsonOut); isSuccess = true; } catch (IOException e) { LOGGER.error(e.getMessage(), e); } return isSuccess; }
From source file:io.seqware.pipeline.plugins.FileProvenanceQueryTool.java
private Path populateOriginalReportFromWS() throws IOException { Map<FileProvenanceParam, List<String>> map = ProvenanceUtility.convertOptionsToMap(options, metadata); // specify some standard filters that are required for filters map.put(FileProvenanceParam.skip, new ImmutableList.Builder<String>().add("false").build()); map.put(FileProvenanceParam.workflow_run_status, new ImmutableList.Builder<String>().add(WorkflowRunStatus.completed.toString()).build()); map.put(FileProvenanceParam.processing_status, new ImmutableList.Builder<String>().add(ProcessingStatus.success.toString()).build()); Path originalReport = Files.createTempFile("file_provenance", "txt"); Log.debug("Original report written to " + originalReport.toString()); try (BufferedWriter originalWriter = Files.newBufferedWriter(originalReport, Charset.defaultCharset())) { metadata.fileProvenanceReport(map, originalWriter); }/*from w w w. j a v a 2 s .c o m*/ return originalReport; }
From source file:org.apache.cassandra.db.VerifyTest.java
protected void writeChecksum(long checksum, String filePath) { File outFile = new File(filePath); BufferedWriter out = null;/*w w w .ja va 2 s.c om*/ try { out = Files.newBufferedWriter(outFile.toPath(), Charsets.UTF_8); out.write(String.valueOf(checksum)); out.flush(); out.close(); } catch (IOException e) { throw new FSWriteError(e, outFile); } finally { FileUtils.closeQuietly(out); } }
From source file:edu.vt.vbi.patric.cache.DataLandingGenerator.java
public boolean createCacheFileTranscriptomics(String filePath) { boolean isSuccess = false; JSONObject jsonData = new JSONObject(); JSONObject data;/*from ww w .ja v a 2 s .co m*/ // from WP // data data = read(baseURL + "/tab/dlp-transcriptomics-data/?req=passphrase"); if (data != null) { jsonData.put("data", data); } // tools data = read(baseURL + "/tab/dlp-transcriptomics-tools/?req=passphrase"); if (data != null) { jsonData.put("tools", data); } // process data = read(baseURL + "/tab/dlp-transcriptomics-process/?req=passphrase"); if (data != null) { jsonData.put("process", data); } // download data = read(baseURL + "/tab/dlp-transcriptomics-download/?req=passphrase"); if (data != null) { jsonData.put("download", data); } // topSpecies data = getTopSpeciesForTranscriptomics(); if (data != null) { jsonData.put("topSpecies", data); } // featuredExperiment data = getFeaturedExperimentForTranscriptomics(); if (data != null) { jsonData.put("featuredExperiment", data); } // popularGenomes data = getPopularGenomesForTranscriptomics(); if (data != null) { jsonData.put("popularGenomes", data); } // save jsonData to file try (PrintWriter jsonOut = new PrintWriter( Files.newBufferedWriter(FileSystems.getDefault().getPath(filePath), Charset.defaultCharset()));) { jsonData.writeJSONString(jsonOut); isSuccess = true; } catch (IOException e) { LOGGER.error(e.getMessage(), e); } return isSuccess; }
From source file:de.upb.timok.run.GenericSmacPipeline.java
private void splitTrainTestFile(String timedInputFile, String timedInputTrainFile, String timedInputTestFile, double trainPercentage, double testPercentage, double anomalyPercentage, boolean isRti) throws IOException { logger.info("TimedInputFile=" + timedInputFile); final File f = new File(timedInputFile); System.out.println(f);//ww w. j av a 2 s.c om final LineNumberReader lnr = new LineNumberReader(new FileReader(timedInputFile)); lnr.skip(Long.MAX_VALUE); int samples = lnr.getLineNumber(); lnr.close(); final int trainingSamples = (int) (samples * trainPercentage); final int testSamples = (int) (samples * testPercentage); final int anomalies = (int) (anomalyPercentage * testSamples); final int writtenTrainingSamples = 0; final int writtenTestSamples = 0; int insertedAnomalies = 0; final BufferedReader br = Files.newBufferedReader(Paths.get(timedInputFile), StandardCharsets.UTF_8); String line = null; final BufferedWriter trainWriter = Files.newBufferedWriter(Paths.get(timedInputTrainFile), StandardCharsets.UTF_8); final BufferedWriter testWriter = Files.newBufferedWriter(Paths.get(timedInputTestFile), StandardCharsets.UTF_8); final Random r = new Random(MasterSeed.nextLong()); final Random mutation = new Random(MasterSeed.nextLong()); boolean force = false; int lineIndex = 0; int linesLeft; int anomaliesToInsert; if (isRti) { br.readLine(); samples--; } while ((line = br.readLine()) != null) { if (writtenTrainingSamples < trainingSamples && writtenTestSamples < testSamples) { // choose randomly according to train/test percentage if (r.nextDouble() > testPercentage) { // write to train writeSample(new TimedSequence(line, true, false).toTrebaString(), trainWriter); } else { // write to test insertedAnomalies = testAndWriteAnomaly(anomalies, insertedAnomalies, anomalyPercentage, line, testWriter, mutation, force); } } else if (writtenTrainingSamples >= trainingSamples) { insertedAnomalies = testAndWriteAnomaly(anomalies, insertedAnomalies, anomalyPercentage, line, testWriter, mutation, force); } else if (writtenTestSamples >= testSamples) { // only write trainSamples from now on writeSample(new TimedSequence(line, true, false).toTrebaString(), trainWriter); } lineIndex++; linesLeft = samples - lineIndex; anomaliesToInsert = anomalies - insertedAnomalies; if (linesLeft <= anomaliesToInsert) { force = true; } } br.close(); trainWriter.close(); testWriter.close(); }
From source file:br.bireme.ngrams.NGrams.java
/** * * @param index//ww w .j av a 2 s .c o m * @param schema * @param inFile * @param inFileEncoding * @param outFile * @param outFileEncoding * @throws IOException * @throws ParseException */ public static void search(final NGIndex index, final NGSchema schema, final String inFile, final String inFileEncoding, final String outFile, final String outFileEncoding) throws IOException, ParseException { if (index == null) { throw new NullPointerException("index"); } if (schema == null) { throw new NullPointerException("schema"); } if (inFile == null) { throw new NullPointerException("inFile"); } if (inFileEncoding == null) { throw new NullPointerException("inFileEncoding"); } if (outFile == null) { throw new NullPointerException("outFile"); } if (outFileEncoding == null) { throw new NullPointerException("outFileEncoding"); } final Charset inCharset = Charset.forName(inFileEncoding); final Charset outCharset = Charset.forName(outFileEncoding); final IndexSearcher searcher = index.getIndexSearcher(); final NGAnalyzer analyzer = (NGAnalyzer) index.getAnalyzer(); final Parameters parameters = schema.getParameters(); final NGramDistance ngDistance = new NGramDistance(analyzer.getNgramSize()); final Set<String> id_id = new HashSet<>(); int cur = 0; try (final BufferedReader reader = Files.newBufferedReader(new File(inFile).toPath(), inCharset); final BufferedWriter writer = Files.newBufferedWriter(new File(outFile).toPath(), outCharset)) { writer.append("rank|similarity|search_doc_id|index_doc_id|" + "ngram_search_text|ngram_index_text|search_source|" + "index_source\n"); final Set<Result> results = new HashSet<>(); while (true) { final String line = reader.readLine(); if (line == null) { break; } if (++cur % 250 == 0) { System.out.println("<<< " + cur); } results.clear(); final String tline = line.replace(':', ' ').trim(); if (!tline.isEmpty()) { final String[] split = tline.split(" *\\| *", Integer.MAX_VALUE); if (split.length != parameters.nameFields.size()) { throw new IOException("invalid number of fields: " + line); } searchRaw(parameters, searcher, analyzer, ngDistance, tline, true, id_id, results); if (!results.isEmpty()) { writeOutput(parameters, results, writer); } } } searcher.getIndexReader().close(); } }