Java tutorial
/* * Copyright 2015 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. */ package org.opencb.opencga.catalog.utils; import org.apache.commons.lang3.math.NumberUtils; import org.opencb.opencga.catalog.models.File; import java.io.BufferedReader; import java.io.FileInputStream; import java.io.IOException; import java.io.InputStreamReader; import java.net.URI; import java.nio.file.Files; import java.nio.file.Path; import java.nio.file.Paths; /** * Created by ralonso on 12/03/15. */ public class BioformatDetector { // protected static final Map<File.Bioformat, Pattern> bioformatMap = new HashMap<>(); // static { // bioformatMap.put(File.Bioformat.ALIGNMENT, Pattern.compile(".*\\.(bam|sam|cram)(\\.[\\w]+)*", Pattern.CASE_INSENSITIVE)); // bioformatMap.put(File.Bioformat.VARIANT, Pattern.compile(".*\\.(vcf)(\\.[\\w]+)*", Pattern.CASE_INSENSITIVE)); // bioformatMap.put(File.Bioformat.PEDIGREE, Pattern.compile(".*\\.(ped)(\\.[\\w]+)*", Pattern.CASE_INSENSITIVE)); // } public static File.Bioformat detect(URI uri) { return detect(uri, FormatDetector.detect(uri), CompressionDetector.detect(uri)); } public static File.Bioformat detect(URI uri, File.Format format, File.Compression compression) { String path = uri.getPath(); Path source = Paths.get(uri); String mimeType; try { switch (format) { case VCF: case GVCF: case BCF: return File.Bioformat.VARIANT; case TBI: break; case SAM: case BAM: case CRAM: return File.Bioformat.ALIGNMENT; case BAI: return File.Bioformat.NONE; //TODO: Alignment? case FASTQ: return File.Bioformat.SEQUENCE; case PED: return File.Bioformat.PEDIGREE; case TAB_SEPARATED_VALUES: break; case COMMA_SEPARATED_VALUES: break; case PROTOCOL_BUFFER: break; case PLAIN: break; case JSON: case AVRO: String file; if (compression != File.Compression.NONE) { file = com.google.common.io.Files.getNameWithoutExtension(uri.getPath()); //Remove compression extension file = com.google.common.io.Files.getNameWithoutExtension(file); //Remove format extension } else { file = com.google.common.io.Files.getNameWithoutExtension(uri.getPath()); //Remove format extension } if (file.endsWith("variants")) { return File.Bioformat.VARIANT; } else if (file.endsWith("alignments")) { return File.Bioformat.ALIGNMENT; } break; case PARQUET: break; case IMAGE: case BINARY: case EXECUTABLE: case UNKNOWN: case XML: return File.Bioformat.NONE; default: break; } // for (Map.Entry<File.Bioformat, Pattern> entry : bioformatMap.entrySet()) { // if (entry.getValue().matcher(path).matches()) { // return entry.getKey(); // } // } mimeType = Files.probeContentType(source); if (path.endsWith(".nw")) { return File.Bioformat.OTHER_NEWICK; } if (mimeType == null || !mimeType.equalsIgnoreCase("text/plain") || path.endsWith(".redirection") || path.endsWith(".Rout") || path.endsWith("cel_files.txt") || !path.endsWith(".txt")) { return File.Bioformat.NONE; } FileInputStream fstream = new FileInputStream(path); BufferedReader br = new BufferedReader(new InputStreamReader(fstream)); String strLine; int numberOfLines = 20; int i = 0; boolean names = false; while ((strLine = br.readLine()) != null) { if (strLine.equalsIgnoreCase("")) { continue; } if (i == numberOfLines) { break; } if (strLine.startsWith("#")) { if (strLine.startsWith("#NAMES")) { names = true; } else { continue; } } else { String[] fields = strLine.split("\t"); if (fields.length > 2) { if (names && NumberUtils.isNumber(fields[1])) { return File.Bioformat.DATAMATRIX_EXPRESSION; } } else if (fields.length == 1) { if (fields[0].split(" ").length == 1 && !NumberUtils.isNumber(fields[0])) { return File.Bioformat.IDLIST; } } else if (fields.length == 2) { if (!fields[0].contains(" ") && NumberUtils.isNumber(fields[1])) { return File.Bioformat.IDLIST_RANKED; } } } i++; } br.close(); } catch (IOException e) { e.printStackTrace(); } return File.Bioformat.NONE; } }